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3edc

Crystal Structure of a 1.6-hexanediol Bound Tetrameric Form of Escherichia coli Lac-repressor Refined to 2.1 Resolution

Method: X-RAY DIFFRACTION Dmax: 95.2 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Lactose operon repressor

Escherichia coli K12

UniProt P03023

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–360 Chain B； UniProt 1–360 Chain C； UniProt 1–360 Chain D； UniProt 1–360 Not recorded HEZ HEXANE-1,6-DIOL × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；microseeded, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 2.10 Å R-free 0.201

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 3EDC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CJG NMR STRUCTURE OF LAC REPRESSOR HP62-DNA COMPLEX Deposited 1999-04-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–62（62 aa） Fragment：HEADPIECE, RESIDUES 1 - 62
Chain B 1–62（62 aa） Fragment：HEADPIECE, RESIDUES 1 - 62
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.1；315 K；Ionic strength (raw mmCIF value) SEE ARTICLE；Pressure 1
NMR sample composition SEE ARTICLE
Resolution not provided
1EFA CRYSTAL STRUCTURE OF THE LAC REPRESSOR DIMER BOUND TO OPERATOR AND THE ANTI-INDUCER ONPF Deposited 2000-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–333（333 aa） Fragment：RESIDUES 1-333
Chain B 1–333（333 aa） Fragment：RESIDUES 1-333
Mutation：ALA109THR Mutation：ALA109THR NPF 2-nitrophenyl beta-D-fucopyranoside × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；ammonium sulfate, PEG 400, HEPES, Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.60 Å R-free 0.264
1EFA CRYSTAL STRUCTURE OF THE LAC REPRESSOR DIMER BOUND TO OPERATOR AND THE ANTI-INDUCER ONPF Deposited 2000-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–333（333 aa） Fragment：RESIDUES 1-333
Mutation：ALA109THR NPF 2-nitrophenyl beta-D-fucopyranoside × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；ammonium sulfate, PEG 400, HEPES, Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.60 Å R-free 0.264
1JWL Structure of the Dimeric lac Repressor/Operator O1/ONPF Complex Deposited 2001-09-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–333（333 aa） Fragment：C-terminal deletion mutant
Chain B 1–333（333 aa） Fragment：C-terminal deletion mutant
Not recorded NPF 2-nitrophenyl beta-D-fucopyranoside × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；ammonium sulfate, PEG400, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 4.00 Å R-free 0.261
1JWL Structure of the Dimeric lac Repressor/Operator O1/ONPF Complex Deposited 2001-09-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–333（333 aa） Fragment：C-terminal deletion mutant
Not recorded NPF 2-nitrophenyl beta-D-fucopyranoside × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；ammonium sulfate, PEG400, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 4.00 Å R-free 0.261
1JYE Structure of a Dimeric Lac Repressor with C-terminal Deletion and K84L Substitution Deposited 2001-09-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–349（349 aa） Fragment：C-TERMINAL DELETION MUTANT
Mutation：YES GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；Sodium Acetate, Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.70 Å R-free 0.241
1JYF Structure of the Dimeric Lac Repressor with an 11-residue C-terminal Deletion. Deposited 2001-09-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–349（349 aa） Fragment：C-TERMINAL DELETION
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；Sodium Citrate, Sodium Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.00 Å R-free 0.252
1L1M SOLUTION STRUCTURE OF A DIMER OF LAC REPRESSOR DNA-BINDING DOMAIN COMPLEXED TO ITS NATURAL OPERATOR O1 Deposited 2002-02-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–62（62 aa） Fragment：N-terminal DNA-binding domain, Residues 1-62
Chain B 1–62（62 aa） Fragment：N-terminal DNA-binding domain, Residues 1-62
Mutation：V52C Mutation：V52C No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；315 K；Ionic strength (raw mmCIF value) 10mM KPi, 20mM KCl；Pressure ambient
NMR sample composition 2mM Lac-HP62-V52C U-15N,13C, 10mM KPi, 20mM KCl, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
1LBG LACTOSE OPERON REPRESSOR BOUND TO 21-BASE PAIR SYMMETRIC OPERATOR DNA, ALPHA CARBONS ONLY Deposited 1996-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–360（360 aa）
Chain B 1–360（360 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 4.80 Å
1LBG LACTOSE OPERON REPRESSOR BOUND TO 21-BASE PAIR SYMMETRIC OPERATOR DNA, ALPHA CARBONS ONLY Deposited 1996-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain C 1–360（360 aa）
Chain D 1–360（360 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 4.80 Å
1LBH INTACT LACTOSE OPERON REPRESSOR WITH GRATUITOUS INDUCER IPTG Deposited 1996-02-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–360（360 aa）
Chain B 1–360（360 aa）
Chain C 1–360（360 aa）
Chain D 1–360（360 aa）
Not recorded IPT 1-methylethyl 1-thio-beta-D-galactopyranoside × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.20 Å
1LBI LAC REPRESSOR Deposited 1996-02-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–360（360 aa）
Chain B 1–360（360 aa）
Chain C 1–360（360 aa）
Chain D 1–360（360 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å
1LCC STRUCTURE OF THE COMPLEX OF LAC REPRESSOR HEADPIECE AND AN 11 BASE-PAIR HALF-OPERATOR DETERMINED BY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS Deposited 1993-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–51（51 aa）
Not recorded NA SODIUM ION × 1 SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1LCD STRUCTURE OF THE COMPLEX OF LAC REPRESSOR HEADPIECE AND AN 11 BASE-PAIR HALF-OPERATOR DETERMINED BY NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND RESTRAINED MOLECULAR DYNAMICS Deposited 1993-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–51（51 aa）
Not recorded NA SODIUM ION × 1 SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1LQC LAC REPRESSOR HEADPIECE (RESIDUES 1-56), NMR, 32 STRUCTURES Deposited 1996-08-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–56（56 aa） Fragment：HEADPIECE, RESIDUES 1 - 56
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1OSL Solution structure of a dimeric lactose DNA-binding domain complexed to a nonspecific DNA sequence Deposited 2003-03-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–62（62 aa） Fragment：N-terminal DNA-binding domain, residues 1-62
Chain B 1–62（62 aa） Fragment：N-terminal DNA-binding domain, residues 1-62
Mutation：V52C Mutation：V52C No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.8；300 K；Ionic strength (raw mmCIF value) 400mM KCl, 60mM KPi；Pressure ambient
NMR sample composition 2mM LAC-HP62-V52C U-15N,13C, 60mM KPI, 400mM KCL | 90% H2O/10% D2O
Resolution not provided
1TLF UNPRECEDENTED QUATERNARY STRUCTURE OF E. COLI LAC REPRESSOR CORE TETRAMER: IMPLICATIONS FOR DNA LOOPING Deposited 1995-03-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 19–319（301 aa）
Chain B 19–319（301 aa）
Chain C 19–319（301 aa）
Chain D 19–319（301 aa）
Not recorded EMC ETHYL MERCURY ION × 4 IPT 1-methylethyl 1-thio-beta-D-galactopyranoside × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å
2BJC NMR structure of a protein-DNA complex of an altered specificity mutant of the lac repressor headpiece that mimics the gal repressor Deposited 2005-02-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–62（62 aa） Fragment：DNA BINDING DOMAIN, LAC HEADPIECE RESIDUES 1-62
Chain B 1–62（62 aa） Fragment：DNA BINDING DOMAIN, LAC HEADPIECE RESIDUES 1-62
Mutation：YES Mutation：YES No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；315 K；Ionic strength (raw mmCIF value) 20；Pressure 1.0
NMR sample composition 95% WATER/5% D2O
Resolution not provided
2KEI Refined Solution Structure of a Dimer of LAC repressor DNA-Binding domain complexed to its natural operator O1 Deposited 2009-01-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–62（62 aa） Fragment：UNP residues 1-62
Chain B 1–62（62 aa） Fragment：UNP residues 1-62
Mutation：V52C Mutation：V52C No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；315 K；Ionic strength (raw mmCIF value) 0.03；Pressure ambient
NMR sample composition 2 mM DNA (5'-D(*DGP*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DGP*DAP*DTP*DAP*DAP*DCP*DAP*DAP*DTP*DTP*DT)-3'), 2 mM DNA (5'-D(P*DAP*DAP*DAP*DTP*DTP*DGP*DTP*DTP*DAP*DTP*DCP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DAP*DAP*DTP*DTP*DC)-3'), 2 mM Lac headpiece dimer, 10% D2O, 10 mM potassium phosphate, 20 mM potassium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2KEJ Solution structure of a dimer of LAC repressor DNA-binding domain complexed to its natural operator O2 Deposited 2009-01-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–62（62 aa） Fragment：UNP residues 1-62
Chain B 1–62（62 aa） Fragment：UNP residues 1-62
Mutation：V52C Mutation：V52C No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；315 K；Ionic strength (raw mmCIF value) 0.03；Pressure ambient
NMR sample composition 0.7 mM DNA (5'-D(*DGP*DAP*DAP*DTP*DTP*DGP*DTP*DGP*DAP*DGP*DCP*DGP*DGP*DAP*DTP*DAP*DAP*DCP*DAP*DAP*DTP*DTP*DT)'), 0.7 mM DNA (5'-D(P*DAP*DAP*DAP*DTP*DTP*DGP*DTP*DTP*DAP*DTP*DCP*DCP*DGP*DCP*DTP*DCP*DAP*DCP*DAP*DAP*DTP*DTP*DC)'), 0.7 mM Lac headpiece dimer, 5% D2O, 10 mM potassium phosphate, 20 mM potassium chloride, 5% U-100% 2H d8-glycerol, 0.01% sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2KEK Solution structure of a dimer of LAC repressor DNA-binding domain complexed to its natural operator O3 Deposited 2009-01-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–62（62 aa） Fragment：UNP residues 1-62
Chain B 1–62（62 aa） Fragment：UNP residues 1-62
Mutation：V52C Mutation：V52C No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；315 K；Ionic strength (raw mmCIF value) 0.03；Pressure ambient
NMR sample composition 0.7 mM DNA (5'-strand1-3'), 0.7 mM DNA (5'-strand2-3'), 0.7 mM Lac headpiece dimer, 5% D2O, 10 mM potassium phosphate, 20 mM potassium chloride, 5% U-100% 2H d8-glycerol, 0.01% sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2P9H High resolution structure of the Lactose Repressor bound to IPTG Deposited 2007-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 62–330（269 aa）
Chain B 62–330（269 aa）
Not recorded IPT 1-methylethyl 1-thio-beta-D-galactopyranoside × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；281 K；1.4 M Sodium Acetate, 0.1 M Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 2.00 Å R-free 0.246
2PAF Crystal Structure of the Lactose Repressor bound to anti-inducer ONPF in induced state Deposited 2007-03-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 62–330（269 aa）
Chain B 62–330（269 aa）
Not recorded NPF 2-nitrophenyl beta-D-fucopyranoside × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；281 K；1.4 M Sodium Acetate, 0.1 M Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.265
2PE5 Crystal Structure of the Lac Repressor bound to ONPG in repressed state Deposited 2007-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 2–331（330 aa） Fragment：sequence database residues 2-331
Chain B 2–331（330 aa） Fragment：sequence database residues 2-331
Mutation：S61L Mutation：S61L 145 2-nitrophenyl beta-D-galactopyranoside × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；281 K；1.8 M Ammonium Sulfate, 0.1 M Hepes pH 7.5. 11% PEG 400, 14% glycerol, 10X ONPG, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.287
2PE5 Crystal Structure of the Lac Repressor bound to ONPG in repressed state Deposited 2007-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain C 2–331（330 aa） Fragment：sequence database residues 2-331
Mutation：S61L 145 2-nitrophenyl beta-D-galactopyranoside × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；281 K；1.8 M Ammonium Sulfate, 0.1 M Hepes pH 7.5. 11% PEG 400, 14% glycerol, 10X ONPG, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.287

21 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LACI_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–360； UniProt 1–360 Author chain B； PDBConstruct 1–360； UniProt 1–360 Author chain C； PDBConstruct 1–360； UniProt 1–360 Author chain D； PDBConstruct 1–360； UniProt 1–360

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

SAXS profile for 3edc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3edc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3edc
Deposition date deposition_date2008-09-03
Structure title titleCrystal Structure of a 1.6-hexanediol Bound Tetrameric Form of Escherichia coli Lac-repressor Refined to 2.1 Resolution
Keywords keywordsLac-repressor, allosteric, tetramer, DNA-binding, Repressor, Transcription, Transcription regulation; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier31.48 Å
Radius of gyration Rg (electron density) rg_electron30.44 Å
Forward intensity I(0) i0263843000.00
Molecular weight molecular_weight128380.0 kDa
Excluded volume excluded_volume160530 ų
Envelope volume envelope_volume194090 ų
Hydration-shell volume shell_volume50508 ų
Envelope diameter envelope_diameter98.9 Å
Shell Rg shell_rg39.52 Å
Envelope Rg envelope_rg30.31 Å
Shape Rg shape_rg30.44 Å
Total Rg total_rg31.16 Å
Total atoms total_atoms8996
Residues n_residues1200
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax95.2 Å
Rg (real space) rg_real31.26 Å
Rg uncertainty (real space) rg_real_error0.45 Å
I(0) (real space) i0_real2.6380e+08
I(0) uncertainty (real space) i0_real_error3.3250e+06
Rg (reciprocal space) rg_reciprocal31.36 Å
I(0) (reciprocal space) i0_reciprocal263900000.0000
Solution quality estimate total_estimate0.9011
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary— Å
Skewness Skewness skewness0.126
Kurtosis Kurtosis kurtosis-0.483
Angular range angular_range— – 0.2500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha95380000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.935
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3edca_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamilyc.93.1 — Periplasmic binding protein-like I
Family Family familyc.93.1.1 — L-arabinose binding protein-like
Domain ID domain_idd3edcb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamilyc.93.1 — Periplasmic binding protein-like I
Family Family familyc.93.1.1 — L-arabinose binding protein-like
Domain ID domain_idd3edcc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamilyc.93.1 — Periplasmic binding protein-like I
Family Family familyc.93.1.1 — L-arabinose binding protein-like
Domain ID domain_idd3edcd_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.93 — Periplasmic binding protein-like I
Superfamily Superfamily superfamilyc.93.1 — Periplasmic binding protein-like I
Family Family familyc.93.1.1 — L-arabinose binding protein-like

CATH v4.4 (8 domains)

Domain ID domain_id3edcA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id3edcA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id3edcB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id3edcB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id3edcC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id3edcC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id3edcD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id3edcD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
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8. Citations (1)

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9. Files and Curves (10)