1xpu

Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic 5a-(3-formylphenylsulfanyl)-dihydrobicyclomycin (FPDB)

Method: X-RAY DIFFRACTION D_max: 149.3 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Rho transcription termination factor

Escherichia coli

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 1–419	Not recorded	5'-R(CPUPCPUPCPUPCPU)-3' × 1 MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.5；293 K；PEG 8000, Na Cacodylate, NaCl, Glycerol, FOS-Choline-12, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.05 Å R-free 0.295
2	Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain B； UniProt 1–419	Not recorded	5'-R(CPUPCPUPCPUPCPU)-3' × 1 MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 FPD 5A-(3-FORMYLPHENYLSULFANYL)-DIHYDROBICYCLOMYCIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.5；293 K；PEG 8000, Na Cacodylate, NaCl, Glycerol, FOS-Choline-12, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.05 Å R-free 0.295
3	Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain C； UniProt 1–419	Not recorded	5'-R(CPUPCPUPCPUPCPU)-3' × 1 MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 FPD 5A-(3-FORMYLPHENYLSULFANYL)-DIHYDROBICYCLOMYCIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.5；293 K；PEG 8000, Na Cacodylate, NaCl, Glycerol, FOS-Choline-12, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.05 Å R-free 0.295
4	Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain D； UniProt 1–419	Not recorded	5'-R(CPUPCPUPCPUPCPU)-3' × 1 MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 FPD 5A-(3-FORMYLPHENYLSULFANYL)-DIHYDROBICYCLOMYCIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.5；293 K；PEG 8000, Na Cacodylate, NaCl, Glycerol, FOS-Choline-12, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.05 Å R-free 0.295
5	Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain E； UniProt 1–419	Not recorded	5'-R(CPUPCPUPCPUPCPU)-3' × 1 MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 FPD 5A-(3-FORMYLPHENYLSULFANYL)-DIHYDROBICYCLOMYCIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.5；293 K；PEG 8000, Na Cacodylate, NaCl, Glycerol, FOS-Choline-12, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.05 Å R-free 0.295
6	Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain F； UniProt 1–419	Not recorded	5'-R(CPUPCPUPCPUPCPU)-3' × 1 MG MAGNESIUM ION × 1 FPD 5A-(3-FORMYLPHENYLSULFANYL)-DIHYDROBICYCLOMYCIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.5；293 K；PEG 8000, Na Cacodylate, NaCl, Glycerol, FOS-Choline-12, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.05 Å R-free 0.295

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1XPU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FYZ METHANE MONOOXYGENASE HYDROXYLASE, FORM II REDUCED BY SOAKING Deposited 2000-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Chain B 1–527（527 aa）	Not recorded	FE2 FE (II) ION × 4 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 8000, CaCl2, MOPS, 1,10-decanedioic acid. pH 7.0, VAPOR DIFFUSION, HANGING DROP at 298 K	Resolution 2.15 Å R-free 0.230
1FZ0 METHANE MONOOXYGENASE HYDROXYLASE, FORM II MIXED-VALENT GROWN ANAEROBICALLY Deposited 2000-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Chain B 1–527（527 aa）	Not recorded	FE2 FE (II) ION × 4 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 8000, CaCl2, MOPS, 1,10-decanedioic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.07 Å R-free 0.230
1FZ1 METHANE MONOOXYGENASE HYDROXYLASE, FORM III OXIDIZED Deposited 2000-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Chain B 1–527（527 aa）	Not recorded	FE FE (III) ION × 4 CA CALCIUM ION × 4 FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 8000, CaCl2, MOPS, 1,10-decanedioic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.96 Å R-free 0.234
1FZ2 METHANE MONOOXYGENASE HYDROXYLASE, FORM II MIXED-VALENT GENERATED BY CRYSTAL SOAKING Deposited 2000-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Chain B 1–527（527 aa）	Not recorded	FE2 FE (II) ION × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 8000, CaCl2, MOPS, 1,10-decanedioic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.15 Å R-free 0.229
1FZ3 METHANE MONOOXYGENASE HYDROXYLASE, FORM III SOAK AT PH 6.2 (0.1 M PIPES) Deposited 2000-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Chain B 1–527（527 aa）	Not recorded	FE FE (III) ION × 4 CA CALCIUM ION × 3 FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 8000, CaCl2, MOPS, 1,10-decanedioic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.03 Å R-free 0.228
1FZ4 METHANE MONOOXYGENASE HYDROXYLASE, FORM III SOAKED AT PH 8.5 (0.1 M TRIS) Deposited 2000-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Chain B 1–527（527 aa）	Not recorded	FE FE (III) ION × 4 CA CALCIUM ION × 3 FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 8000, CaCl2, MOPS, 1,10-decanedioic acid. pH 7.0, VAPOR DIFFUSION, HANGING DROP at 298 K	Resolution 2.38 Å R-free 0.256
1FZ5 METHANE MONOOXYGENASE HYDROXYLASE, FORM II CRYSTALLIZED ANAEROBICALLY FROM REDUCED ENZYME Deposited 2000-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Chain B 1–527（527 aa）	Not recorded	FE2 FE (II) ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 8000, CaCl2, MOPS, 1,10-decanedioic acid. pH 7.0, VAPOR DIFFUSION, HANGING DROP at 298 K	Resolution 2.40 Å R-free 0.253
1FZ6 METHANE MONOOXYGENASE HYDROXYLASE, FORM II SOAKED IN 1 M METHANOL Deposited 2000-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Chain B 1–527（527 aa）	Not recorded	FE FE (III) ION × 4 CA CALCIUM ION × 3 MOH METHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 8000, CaCl2, MOPS, 1,10-decanedioic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 298K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.05 Å R-free 0.244
1FZ7 METHANE MONOOXYGENASE HYDROXYLASE, FORM III SOAKED IN 0.9 M ETHANOL Deposited 2000-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Chain B 1–527（527 aa）	Not recorded	FE FE (III) ION × 4 CA CALCIUM ION × 3 FMT FORMIC ACID × 1 EOH ETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 8000, CaCl2, MOPS, 1,10-decanedioic acid. pH 7.0, VAPOR DIFFUSION, HANGING DROP at 298 K	Resolution 1.96 Å R-free 0.255
1FZ8 METHANE MONOOXYGENASE HYDROXYLASE, FORM II COCRYSTALLIZED WITH DIBROMOMETHANE Deposited 2000-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Chain B 1–527（527 aa）	Not recorded	FE FE (III) ION × 4 CA CALCIUM ION × 3 2BM DIBROMOMETHANE × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 8000, CaCl2, MOPS, 1,10-decanedioic acid, dibromomethane, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 2.10 Å R-free 0.250
1FZ9 Methane monooxygenase hydroxylase, form II cocrystallized with iodoethane Deposited 2000-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Chain B 1–527（527 aa）	Not recorded	FE FE (III) ION × 4 CA CALCIUM ION × 3 ETI IODOETHANE × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 8000, CaCl2, MOPS, 1,10-decanedioic acid, iodoethane. pH 7.0, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 2.30 Å R-free 0.260
1FZH METHANE MONOOXYGENASE HYDROXYLASE, FORM II PRESSURIZED WITH XENON GAS Deposited 2000-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Chain B 1–527（527 aa）	Not recorded	FE FE (III) ION × 4 CA CALCIUM ION × 4 XE XENON × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 8000, CaCl2, MOPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 277K	Resolution 2.60 Å R-free 0.260
1FZI METHANE MONOOXYGENASE HYDROXYLASE, FORM I PRESSURIZED WITH XENON GAS Deposited 2000-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Chain B 1–527（527 aa）	Not recorded	FE FE (III) ION × 4 XE XENON × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 4000, ammonium acetate, Li2SO4, MOPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 277K	Resolution 3.30 Å R-free 0.253
1MMO CRYSTAL STRUCTURE OF A BACTERIAL NON-HAEM IRON HYDROXYLASE THAT CATALYSES THE BIOLOGICAL OXIDATION OF METHANE Deposited 1994-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 15–526（512 aa） Chain E 15–526（512 aa）	Not recorded	FE FE (III) ION × 4 ACY ACETIC ACID × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1MTY METHANE MONOOXYGENASE HYDROXYLASE FROM METHYLOCOCCUS CAPSULATUS (BATH) Deposited 1996-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 15–526（512 aa） Chain E 15–526（512 aa）	Not recorded	FE FE (III) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；25 MM LI2SO4, 50 MM NH4OAC, 5% PEG 4000, IN 25 MM MOPS PH 7.0 WITH A RESERVOIR OF 20% PEG 4000	Resolution 1.70 Å
1XMF Structure of Mn(II)-Soaked Apo Methane Monooxygenase Hydroxylase Crystals from M. capsulatus (Bath) Deposited 2004-10-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Fragment：alpha subunit Chain B 1–527（527 aa） Fragment：alpha subunit	Not recorded	MN MANGANESE (II) ION × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；MOPS, CaCl2, PEG8000, glycerol, azide, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.32 Å R-free 0.263
1XMG Crystal structure of apo methane monooxygenase hydroxylase from M. capsulatus (Bath) Deposited 2004-10-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Fragment：alpha subunit Chain B 1–527（527 aa） Fragment：alpha subunit	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；278 K；MOPS, PEG 8000, calcium chloride, glycerol, azide, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 2.10 Å R-free 0.261
1XMH Structure of Co(II) reconstituted methane monooxygenase hydroxylase from M. capsulatus (Bath) Deposited 2004-10-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Fragment：alpha subunit Chain B 1–527（527 aa） Fragment：alpha subunit	Not recorded	CO COBALT (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；278 K；MOPS, PEG 8000, calcium chloride, sodium azide, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 2.32 Å R-free 0.225
1XPO Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin Deposited 2004-10-09	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–419（419 aa）	Not recorded	MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；PEG 8000, Na Cacodylate, NaCl, glycerol, FOS-choline-12, pH 6.5, VAPOR DIFFUSION, temperature 18K	Resolution 3.15 Å R-free 0.306
1XPO Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin Deposited 2004-10-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–419（419 aa）	Not recorded	MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 BCM BICYCLOMYCIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；PEG 8000, Na Cacodylate, NaCl, glycerol, FOS-choline-12, pH 6.5, VAPOR DIFFUSION, temperature 18K	Resolution 3.15 Å R-free 0.306
1XPO Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin Deposited 2004-10-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain C 1–419（419 aa）	Not recorded	MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 BCM BICYCLOMYCIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；PEG 8000, Na Cacodylate, NaCl, glycerol, FOS-choline-12, pH 6.5, VAPOR DIFFUSION, temperature 18K	Resolution 3.15 Å R-free 0.306
1XPO Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin Deposited 2004-10-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain D 1–419（419 aa）	Not recorded	MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 BCM BICYCLOMYCIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；PEG 8000, Na Cacodylate, NaCl, glycerol, FOS-choline-12, pH 6.5, VAPOR DIFFUSION, temperature 18K	Resolution 3.15 Å R-free 0.306
1XPO Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin Deposited 2004-10-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain E 1–419（419 aa）	Not recorded	MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 BCM BICYCLOMYCIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；PEG 8000, Na Cacodylate, NaCl, glycerol, FOS-choline-12, pH 6.5, VAPOR DIFFUSION, temperature 18K	Resolution 3.15 Å R-free 0.306
1XPO Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin Deposited 2004-10-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain F 1–419（419 aa）	Not recorded	MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 BCM BICYCLOMYCIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；PEG 8000, Na Cacodylate, NaCl, glycerol, FOS-choline-12, pH 6.5, VAPOR DIFFUSION, temperature 18K	Resolution 3.15 Å R-free 0.306
1XPR Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic 5a-formylbicyclomycin (FB) Deposited 2004-10-09	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–419（419 aa）	Not recorded	MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；PEG 3350, Na Cacodylate, NaCl, glycerol, Na DihydrogenPhosphate, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.15 Å R-free 0.296
1XPR Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic 5a-formylbicyclomycin (FB) Deposited 2004-10-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–419（419 aa）	Not recorded	MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 FB 5A-FORMYLBICYCLOMYCIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；PEG 3350, Na Cacodylate, NaCl, glycerol, Na DihydrogenPhosphate, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.15 Å R-free 0.296
1XPR Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic 5a-formylbicyclomycin (FB) Deposited 2004-10-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain C 1–419（419 aa）	Not recorded	MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 FB 5A-FORMYLBICYCLOMYCIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；PEG 3350, Na Cacodylate, NaCl, glycerol, Na DihydrogenPhosphate, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.15 Å R-free 0.296
1XPR Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic 5a-formylbicyclomycin (FB) Deposited 2004-10-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain D 1–419（419 aa）	Not recorded	MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 FB 5A-FORMYLBICYCLOMYCIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；PEG 3350, Na Cacodylate, NaCl, glycerol, Na DihydrogenPhosphate, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.15 Å R-free 0.296
1XPR Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic 5a-formylbicyclomycin (FB) Deposited 2004-10-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain E 1–419（419 aa）	Not recorded	MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 FB 5A-FORMYLBICYCLOMYCIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；PEG 3350, Na Cacodylate, NaCl, glycerol, Na DihydrogenPhosphate, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.15 Å R-free 0.296
1XPR Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic 5a-formylbicyclomycin (FB) Deposited 2004-10-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain F 1–419（419 aa）	Not recorded	MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 FB 5A-FORMYLBICYCLOMYCIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；PEG 3350, Na Cacodylate, NaCl, glycerol, Na DihydrogenPhosphate, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 3.15 Å R-free 0.296
1XU3 Soluble methane monooxygenase hydroxylase-soaked with bromophenol Deposited 2004-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Fragment：alpha subunit Chain B 1–527（527 aa） Fragment：alpha subunit	Not recorded	FE FE (III) ION × 4 BML 4-BROMOPHENOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；273 K；MOPS, PEG 8000, NaN3, CaCl2, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K, pH 7.00	Resolution 2.30 Å R-free 0.245
1XU5 Soluble methane monooxygenase hydroxylase-phenol soaked Deposited 2004-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Fragment：alpha subunit Chain B 1–527（527 aa） Fragment：alpha subunit	Not recorded	FE FE (III) ION × 4 OH HYDROXIDE ION × 2 IPH PHENOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；273 K；MOPS, PEG 8000, NaN3, CaCl2, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 1.96 Å R-free 0.228
1XVB soluble methane monooxygenase hydroxylase: 6-bromohexanol soaked structure Deposited 2004-10-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Chain B 1–527（527 aa）	Not recorded	FE FE (III) ION × 4 BHL 6-BROMOHEXAN-1-OL × 10 BBU 1-BROMOBUTANE × 1 BBX 1-BROMOETHANE × 1 CA CALCIUM ION × 1 3BR 1-BROMOPROPANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；MOPS, PEG 8000, NaN3, CaCl2, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.251
1XVC soluble methane monooxygenase hydroxylase: 8-bromooctanol soaked structure Deposited 2004-10-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Fragment：alpha subunit Chain B 1–527（527 aa） Fragment：alpha subunit	Not recorded	FE FE (III) ION × 4 BR BROMIDE ION × 2 5BR 1-BROMOPENTANE × 1 BMM BROMOMETHANE × 1 FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；MOPS, PEG 8000, NaN3, CaCl2, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.234
1XVD Soluble methane monooxygenase hydroxylase: 4-fluorophenol soaked structure Deposited 2004-10-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Fragment：alpha subunit Chain B 1–527（527 aa） Fragment：alpha subunit	Not recorded	FE FE (III) ION × 4 FPN 4-FLUOROPHENOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；273 K；MOPS, PEG 8000, CaCl2, NaN3, glyerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 2.30 Å R-free 0.229
1XVE soluble methane monooxygenase hydroxylase: 3-bromo-3-butenol soaked structure Deposited 2004-10-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Fragment：alpha subunit Chain B 1–527（527 aa） Fragment：alpha subunit	Not recorded	FE FE (III) ION × 4 CA CALCIUM ION × 2 3BB 3-BROMOBUT-3-EN-1-OL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；MOPS, PEG 8000, NaN3, CaCl2, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.40 Å R-free 0.260
1XVF soluble methane monooxygenase hydroxylase: chloropropanol soaked structure Deposited 2004-10-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Fragment：alpha subunit Chain B 1–527（527 aa） Fragment：alpha subunit	Not recorded	FE FE (III) ION × 4 3CL 3-CHLOROPROPANOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；MOPS, PEG 8000, NaN3, CaCl2, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.230
1XVG soluble methane monooxygenase hydroxylase: bromoethanol soaked structure Deposited 2004-10-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–527（527 aa） Fragment：alpha subunit Chain B 1–527（527 aa） Fragment：alpha subunit	Not recorded	FE FE (III) ION × 4 CA CALCIUM ION × 4 BRJ 2-BROMOETHANOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；MOPS, PEG 8000, CaCl2, NaN3, glyerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.96 Å R-free 0.230
4GAM Complex structure of Methane monooxygenase hydroxylase and regulatory subunit Deposited 2012-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–527（527 aa） Chain F 1–527（527 aa）	Not recorded	FE FE (III) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M MES and 15% PEG 20,000 (w/v) ure 298K, pH 6.5, VAPOR DIFFUSION, SITTING DROP	Resolution 2.90 Å R-free 0.258
4GAM Complex structure of Methane monooxygenase hydroxylase and regulatory subunit Deposited 2012-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain K 1–527（527 aa） Chain P 1–527（527 aa）	Not recorded	FE FE (III) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M MES and 15% PEG 20,000 (w/v) ure 298K, pH 6.5, VAPOR DIFFUSION, SITTING DROP	Resolution 2.90 Å R-free 0.258
7TC7 Cryo-EM structure of methane monooxygenase hydroxylase (by quantifoil) Deposited 2021-12-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–527（527 aa） Chain E 1–527（527 aa）	Not recorded	FE FE (III) ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7；30 mM HEPES, pH 7, 150 mM NaCl, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7TC8 Cryo-EM structure of methane monooxygenase hydroxylase (by graphene) Deposited 2021-12-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 1–527（527 aa） Chain E 1–527（527 aa）	Not recorded	FE FE (III) ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7；30 mM HEPES, pH 7, 150 mM NaCl, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.40 Å

31 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MEMA_METCA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–419； UniProt 1–419 Author chain B； PDBConstruct 1–419； UniProt 1–419 Author chain C； PDBConstruct 1–419； UniProt 1–419 Author chain D； PDBConstruct 1–419； UniProt 1–419 Author chain E； PDBConstruct 1–419； UniProt 1–419 Author chain F； PDBConstruct 1–419； UniProt 1–419

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1xpu
Deposition date deposition_date	2004-10-09
Structure title title	Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic 5a-(3-formylphenylsulfanyl)-dihydrobicyclomycin (FPDB)
Keywords keywords	Rho transcription termination factor; 5a-(3-formylphenylsulfanyl)-dihydrobicyclomycin (FPDB); ATPgammaS, TRANSCRIPTION-RNA COMPLEX; TRANSCRIPTION/RNA
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	46.97 Å
Radius of gyration Rg (electron density) rg_electron	46.41 Å
Forward intensity I(0) i0	1195530000.00
Molecular weight molecular_weight	283770.0 kDa
Excluded volume excluded_volume	354100 Å³
Envelope volume envelope_volume	502510 Å³
Hydration-shell volume shell_volume	85653 Å³
Envelope diameter envelope_diameter	151.1 Å
Shell Rg shell_rg	55.48 Å
Envelope Rg envelope_rg	45.42 Å
Shape Rg shape_rg	46.41 Å
Total Rg total_rg	46.73 Å
Total atoms total_atoms	19853
Residues n_residues	2459
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	149.3 Å
Rg (real space) rg_real	46.69 Å
Rg uncertainty (real space) rg_real_error	0.93 Å
I(0) (real space) i0_real	1.1960e+09
I(0) uncertainty (real space) i0_real_error	2.1550e+07
Rg (reciprocal space) rg_reciprocal	46.97 Å
I(0) (reciprocal space) i0_reciprocal	1196000000.0000
Solution quality estimate total_estimate	0.8978
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	65.9 Å
Skewness Skewness skewness	0.062
Kurtosis Kurtosis kurtosis	-0.630
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	157200000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.935

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	5'-R(CPUPCPUPCPUPCPU)-3'
Molecular weight formula_weight	2400.4 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	G,M,H,J,K,L
Atom count atom_count	19873

CUCUCUCU

Entity 2 Entity 2 polymer

Description description	Rho transcription termination factor
Molecular weight formula_weight	47070.2 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F

MNLTELKNTPVSELITLGENMGLENLARMRKQDIIFAILKQHAKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNFDKPENARNKILFENLTPLHANSRLRMERGNGSTEDLTARVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRLARAYNTVVPASGKVLTGGVDANALHRPKRFFGAARNVEEGGSLTIIATALIDTGSKMDEVIYEEFKGTGNMELHLSRKIAEKRVFPAIDYNRSGTRKEELLTTQEELQKMWILRKIIHPMGEIDAMEFLINKLAMTKTNDDFFEMMKRS

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	5A-(3-FORMYLPHENYLSULFANYL)-DIHYDROBICYCLOMYCIN
Molecular weight formula_weight	440.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	20

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7. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (18 domains)

Domain ID domain_id	d1xpua1
Class class	a — All alpha proteins
Fold Fold fold	a.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamily	a.140.3 — Rho N-terminal domain-like
Family Family family	a.140.3.1 — Rho termination factor, N-terminal domain

Domain ID domain_id	d1xpua2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d1xpua3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d1xpub1
Class class	a — All alpha proteins
Fold Fold fold	a.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamily	a.140.3 — Rho N-terminal domain-like
Family Family family	a.140.3.1 — Rho termination factor, N-terminal domain

Domain ID domain_id	d1xpub2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d1xpub3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d1xpuc1
Class class	a — All alpha proteins
Fold Fold fold	a.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamily	a.140.3 — Rho N-terminal domain-like
Family Family family	a.140.3.1 — Rho termination factor, N-terminal domain

Domain ID domain_id	d1xpuc2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d1xpuc3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d1xpud1
Class class	a — All alpha proteins
Fold Fold fold	a.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamily	a.140.3 — Rho N-terminal domain-like
Family Family family	a.140.3.1 — Rho termination factor, N-terminal domain

Domain ID domain_id	d1xpud2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d1xpud3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d1xpue1
Class class	a — All alpha proteins
Fold Fold fold	a.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamily	a.140.3 — Rho N-terminal domain-like
Family Family family	a.140.3.1 — Rho termination factor, N-terminal domain

Domain ID domain_id	d1xpue2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d1xpue3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d1xpuf1
Class class	a — All alpha proteins
Fold Fold fold	a.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamily	a.140.3 — Rho N-terminal domain-like
Family Family family	a.140.3.1 — Rho termination factor, N-terminal domain

Domain ID domain_id	d1xpuf2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d1xpuf3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

CATH v4.4 (12 domains)

Domain ID domain_id	1xpuA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	1xpuA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1xpuB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	1xpuB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1xpuC01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	1xpuC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1xpuD01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	1xpuD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1xpuE01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	1xpuE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1xpuF01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	1xpuF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	119.477 Å
Unit-cell length b length_b	206.935 Å
Unit-cell length c length_c	148.607 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.95 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.050 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2878
R_work r_work	0.2759
R_free r_free	0.2949

fit	/app/data/saxs_computation/xp/1xpu/1xpu.fit
pddf	/app/data/pr_computation/xp/1xpu/1xpu.pr.out
profile	/app/data/saxs_computation/xp/1xpu/1xpu.dat

Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic 5a-(3-formylphenylsulfanyl)-dihydrobicyclomycin (FPDB)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Rho transcription termination factor

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (18 domains)

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)