4nzg

Crystal Structure of the N-terminal domain of Moloney murine leukemia virus integrase, Northeast Structural Genomics Consortium Target OR3

Method: X-RAY DIFFRACTION D_max: 84.8 Å Quality: GOOD

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

Integrase p46

Moloney murine leukemia virus

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 1338–1435 Chain B； UniProt 1338–1435 Chain C； UniProt 1338–1435 Chain D； UniProt 1338–1435	Not recorded	ZN ZINC ION × 4 ACT ACETATE ION × 3 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 9	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:1.0 M K2HPO4, 0.1 M NaAc, 0.05% Anapoe X-305, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.15 Å R-free 0.265
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1338–1435 Chain C； UniProt 1338–1435	Not recorded	ZN ZINC ION × 2 ACT ACETATE ION × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:1.0 M K2HPO4, 0.1 M NaAc, 0.05% Anapoe X-305, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.15 Å R-free 0.265
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1338–1435 Chain D； UniProt 1338–1435	Not recorded	ZN ZINC ION × 2 ACT ACETATE ION × 2 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:1.0 M K2HPO4, 0.1 M NaAc, 0.05% Anapoe X-305, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.15 Å R-free 0.265

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 4NZG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D0E CRYSTAL STRUCTURES OF THE N-TERMINAL FRAGMENT FROM MOLONEY MURINE LEUKEMIA VIRUS REVERSE TRANSCRIPTASE COMPLEXED WITH NUCLEIC ACID: FUNCTIONAL IMPLICATIONS FOR TEMPLATE-PRIMER BINDING TO THE FINGERS DOMAIN Deposited 1999-09-09	Different construct 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 144–398（255 aa） Fragment：N-TERMINAL FRAGMENT COMPRISING FINGERS AND PALM DOMAINS Chain B 144–398（255 aa） Fragment：N-TERMINAL FRAGMENT COMPRISING FINGERS AND PALM DOMAINS	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；15% PEG 4000,0.1M NH4CL,0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.298
1D1U USE OF AN N-TERMINAL FRAGMENT FROM MOLONEY MURINE LEUKEMIA VIRUS REVERSE TRANSCRIPTASE TO FACILITATE CRYSTALLIZATION AND ANALYSIS OF A PSEUDO-16-MER DNA MOLECULE CONTAINING G-A MISPAIRS Deposited 1999-09-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 144–398（255 aa） Fragment：FINGERS AND PALM DOMAIN OF MMLV RT	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.30 Å R-free 0.286
1I6J CRYSTAL STRUCTURE OF A PSEUDO-16-MER DNA WITH STACKED GUANINES AND TWO G-A MISPAIRS COMPLEXED WITH THE N-TERMINAL FRAGMENT OF MOLONEY MURINE LEUKEMIA VIRUS REVERSE TRANSCRIPTASE Deposited 2001-03-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 144–398（255 aa） Fragment：N-TERMINAL FRAGMENT	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG 4000, NaCl, ADA, MgCl2, HEPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.252
1MML MECHANISTIC IMPLICATIONS FROM THE STRUCTURE OF A CATALYTIC FRAGMENT OF MMLV REVERSE TRANSCRIPTASE Deposited 1995-07-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 130–394（265 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å R-free 0.257
1N4L A DNA analogue of the polypurine tract of HIV-1 Deposited 2002-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 144–398（255 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG 4000, NaCl, ADA, MgCl2, HEPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 277K	Resolution 2.00 Å R-free 0.269
1NND Arginine 116 is Essential for Nucleic Acid Recognition by the Fingers Domain of Moloney Murine Leukemia Virus Reverse Transcriptase Deposited 2003-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 144–398（255 aa） Fragment：MMLV Reverse Transcriptase	Mutation：R116A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 400, Magnesium Chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.30 Å R-free 0.274
1QAI CRYSTAL STRUCTURES OF THE N-TERMINAL FRAGMENT FROM MOLONEY MURINE LEUKEMIA VIRUS REVERSE TRANSCRIPTASE COMPLEXED WITH NUCLEIC ACID: FUNCTIONAL IMPLICATIONS FOR TEMPLATE-PRIMER BINDING TO THE FINGERS DOMAIN Deposited 1999-03-12	Different construct 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 130–394（265 aa） Fragment：FINGERS AND PALM DOMAINS OF THE MMLV REVERSE TRANSCRIPTASE Chain B 130–394（265 aa） Fragment：FINGERS AND PALM DOMAINS OF THE MMLV REVERSE TRANSCRIPTASE	Not recorded	HG MERCURY (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% PEG 4000, 0.1M NH4CL, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.296
1QAJ CRYSTAL STRUCTURES OF THE N-TERMINAL FRAGMENT FROM MOLONEY MURINE LEUKEMIA VIRUS REVERSE TRANSCRIPTASE COMPLEXED WITH NUCLEIC ACID: FUNCTIONAL IMPLICATIONS FOR TEMPLATE-PRIMER BINDING TO THE FINGERS DOMAIN Deposited 1999-03-18	Different construct 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 144–398（255 aa） Fragment：N-TERMINAL FRAGMENT COMPRISING FINGERS AND PALM DOMAINS Chain B 144–398（255 aa） Fragment：N-TERMINAL FRAGMENT COMPRISING FINGERS AND PALM DOMAINS	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；15% PEG 4000, 0.1 M NH4CL,0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.259
1ZTT Netropsin bound to d(CTTAATTCGAATTAAG) in complex with MMLV RT catalytic fragment Deposited 2005-05-27	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: hexameric	Chain A 144–398（255 aa） Fragment：RT catalytic fragment	Not recorded	NT NETROPSIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 4000, magnesium acetate, ADA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.85 Å R-free 0.246
1ZTW d(CTTAATTCGAATTAAG) complexed with Moloney Murine Leukemia Virus Reverse Transcriptase catalytic fragment Deposited 2005-05-27	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: hexameric	Chain A 144–398（255 aa） Fragment：RT catalytic fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 4000, magnesium acetate, ADA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.264
2FJV RT29 Bound to D(CTTAATTCGAATTAAG) in complex with MMLV RT Catalytic Fragment Deposited 2006-01-03	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: hexameric	Chain A 144–398（255 aa） Fragment：RT catalytic domain	Not recorded	HXL 2-(4-(4-CARBAMIMIDOYLPHENOXY)PHENYL)-1H-BENZO[D]IMIDAZOLE-6-CARBOXIMIDAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 4000, MAGNESIUM ACETATE, ADA PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.05 Å R-free 0.280
2FJW d(CTTGAATGCATTCAAG) in complex with MMLV RT catalytic fragment Deposited 2006-01-03	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: hexameric	Chain A 144–398（255 aa）	Mutation：RT catalytic domain	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；PEG 4000, MAGNESIUM ACETATE, ADA, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 1.95 Å R-free 0.256
2FJX RT29 bound to D(CTTGAATGCATTCAAG) in complex with MMLV RT catalytic fragment Deposited 2006-01-03	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: hexameric	Chain A 144–398（255 aa） Fragment：RT catalytic domain	Not recorded	HXL 2-(4-(4-CARBAMIMIDOYLPHENOXY)PHENYL)-1H-BENZO[D]IMIDAZOLE-6-CARBOXIMIDAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 4000, magnesium acetate, ADA pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.266
2FVP A Structural Study of the CA Dinucleotide Step in the Integrase Processing Site of Moloney Murine Leukemia Virus Deposited 2006-01-31	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 144–398（255 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 4000, magnesium acetate, ADA pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.25 Å R-free 0.288
2FVQ A Structural Study of the CA Dinucleotide Step in the Integrase Processing Site of Moloney Murine Leukemia Virus Deposited 2006-01-31	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 144–398（255 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 4000, magnesium acetate, ADA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.263
2FVR A Structural Study of the CA Dinucleotide Step in the Integrase Processing Site of Moloney Murine Leukemia Virus Deposited 2006-01-31	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 144–398（255 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 4000, magnesium acetate, ADA pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.259
2FVS A Structural Study of the CA Dinucleotide Step in the Integrase Processing Site of Moloney Murine Leukemia Virus Deposited 2006-01-31	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 144–398（255 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 4000, magnesium acetate, ADA pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.35 Å R-free 0.265
2HB5 Crystal Structure of the Moloney Murine Leukemia Virus RNase H Domain Deposited 2006-06-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 618–791（174 aa） Fragment：RNase H Domain (Residues 618-791)	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；15% PEG 4000, 0.1M ammonium sulfate, 150mM NaCl, 1.25%PEG-MME 550, 1% 2-propanol, 0.5mM zinc sulfate, 5mM MES , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.59 Å R-free 0.221
2M9U Solution NMR structure of the C-terminal domain (CTD) of Moloney murine leukemia virus integrase, Northeast Structural Genomics Target OR41A Deposited 2013-06-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1659–1738（80 aa） Fragment：DNA binding C terminal domain (CTD) residues 1659-1738	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50mM K-glutamate, 100mM NaCl；Pressure ambient NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] MLV IN CTD, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-10% 13C; U-100% 15N] MLV IN CTD, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2MQV Solution NMR structure of the U5-primer binding site (U5-PBS) domain of murine leukemia virus RNA genome bound to the retroviral nucleocapsid protein Deposited 2014-06-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 479–534（56 aa）	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 7；311 K；Ionic strength (raw mmCIF value) 10mM Tris, 10mM Nacl；Pressure ambient NMR measurement conditions pH 7；288 K；Ionic strength (raw mmCIF value) 10mM Tris, 10mM NaCl；Pressure ambient NMR sample composition 0.5 mM 15N,13C-Alab U5-PBS-NC, 0.5 mM 15N.13C-Glab U5-PBS-NC, 0.5 mM 15N.13C-Ulab U5-PBS-NC, 0.5 mM 15N.13C-Clab U5-PBS-NC, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM U5-PBS-M2-NC, 100% D2O \| 100% D2O NMR sample composition 1 mM UAUCG-linker, 100% D2O \| 100% D2O	Resolution not provided
2MS0 Solution NMR structure pf tRNApro:MLV-Nucleocapsid (1:2) Complex Deposited 2014-07-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 479–534（56 aa） Chain C 479–534（56 aa）	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7.2；311 K；Ionic strength (raw mmCIF value) 10mM Tris, 1mM MgCl2, 10mM NaCl；Pressure ambient NMR sample composition 0.5 mM NC-tRNApro (1:1), 0.5 mM 13C, 15N G-lab tRNA-pro NC-tRNApro (1:1), 0.5 mM 13C, 15N G-lab tRNA-pro NC-tRNApro (1:1), 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2MS1 Solution NMR structure of tRNApro:MLV Nucleocapsid Protein (1:1) Complex Deposited 2014-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 479–534（56 aa）	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 7.2；311 K；Ionic strength (raw mmCIF value) 10mM Tris, 1mM MgCl2, 10mM NaCl；Pressure ambient NMR sample composition 0.5 mM NC-tRNApro (1:1), 0.5 mM 13C, 15N G-lab tRNA-pro NC-tRNApro (1:1), 0.5 mM 13C, 15N G-lab tRNA-pro13C NC-tRNApro (1:1), 0.5 mM 13C, 15N G-lab tRNA-pro NC-tRNApro (1:1), 0.5 mM 13C, 15N G-lab tRNA-13C NC-tRNApro (1:1), 0.5 mM 13C, 15N G-lab tRNA-pro NC-tRNApro (1:1), 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2R2R d(ATTAGTTATAACTAAT) complexed with MMLV RT catalytic fragment Deposited 2007-08-27	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: hexameric	Chain A 144–398（255 aa） Fragment：residues 144-398	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；PEG 4000, MgCl2, pH 6.5, vapor diffusion, temperature 293K	Resolution 2.10 Å R-free 0.269
2R2S Co(III)bleomycinB2 bound to d(ATTAGTTATAACTAAT) complexed with MMLV RT catalytic fragment Deposited 2007-08-27	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: hexameric	Chain A 144–398（255 aa） Fragment：residues 144-398	Not recorded	3CO COBALT (III) ION × 2 BLB BLEOMYCIN B2 × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；PEG 4000, MgCl2, pH 6.5, vapor diffusion, temperature 293K	Resolution 2.80 Å R-free 0.308
2R2T d(ATTTAGTTAACTAAAT) complexed with MMLV RT catalytic fragment Deposited 2007-08-27	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: hexameric	Chain A 144–398（255 aa） Fragment：residues 144-398	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；PEG 4000, MgCl2, pH 6.5, vapor diffusion, temperature 293K	Resolution 2.00 Å R-free 0.264
2R2U Co(III)bleomycinB2 bithiazole/C-terminal tail domain bound to d(ATTTAGTTAACTAAAT) complexed with MMLV RT catalytic fragment Deposited 2007-08-27	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: hexameric	Chain A 144–398（255 aa） Fragment：residues 144-398	Not recorded	BTZ N-(4-{[amino(imino)methyl]amino}butyl)-2,4'-bi-1,3-thiazole-4-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；PEG 4000, MgCl2, pH 6.5, vapor diffusion, temperature 293K	Resolution 2.30 Å R-free 0.282
3FSI Crystal structure of a trypanocidal 4,4'-Bis(imidazolinylamino)diphenylamine bound to DNA Deposited 2009-01-09	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: hexameric	Chain A 144–398（255 aa） Fragment：Reverse transcriptase domain: UNP residues 144-398	Not recorded	ACT ACETATE ION × 10 MWB N1-(4,5-dihydro-1H-imidazol-2-yl)-N4-(4-((4,5-dihydro-1H-imidazol-2-yl)amino)phenyl)benzene-1,4-diamine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 4000, Magnesium acetate, ADA pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.75 Å R-free 0.254
3NNQ Crystal Structure of the N-terminal domain of Moloney murine leukemia virus integrase, Northeast Structural Genomics Consortium Target OR3 Deposited 2010-06-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1331–1435（105 aa） Fragment：N-terminal domain Chain B 1331–1435（105 aa） Fragment：N-terminal domain	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 4 ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；2.0 M Sodium Malonate, 0.1 M Sodium Acetate,0.05% Anapoe X-305, pH 5.0, vapor diffusion, hanging drop, temperature 298K	Resolution 2.69 Å R-free 0.274
4M94 d(ATCCGTTATAACGGAT) complexed with Moloney Murine Leukemia virus reverse transcriptase catalytic fragment Deposited 2013-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 683–937（255 aa） Fragment：UNP residues 683-937	Not recorded	EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；7% PEG 4000, 5mM Magnesium acetate, 50mM N-(2-acetamido)iminodiacetic acid, pH 6.5, vapor diffusion, hanging drop, temperature 293.15K	Resolution 2.14 Å R-free 0.239
4M95 d(ATCCGTTATAACGGAT)complexed with Moloney Murine Leukemia virus reverse transcriptase catalytic fragment Deposited 2013-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 683–937（255 aa） Fragment：UNP residues 683-937	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；9% PEG 4000, 5mM Magnesium acetate, 50mM N-(2-acetamido)iminodiacetic acid, pH 6.5, vapor diffusion, hanging drop, temperature 293.15K	Resolution 1.72 Å R-free 0.234
4MH8 The crystal structure of the monomeric reverse transcriptase from moloney murine leukemia virus Deposited 2013-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 683–1330（648 aa）	Mutation：L435K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；POTASSIUM CHLORIDE, MAGNESIUM ACETATE, SODIUM CACODYLATE, PEG 8000, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 300	Resolution 3.00 Å R-free 0.277
4XO0 Crystal structure of 5'-CTTATPPTAZZATAAG in a host-guest complex Deposited 2015-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 683–937（255 aa） Fragment：unp residues 683-937	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 4000	Resolution 1.70 Å R-free 0.240
4XPC Crystal structure of 5'- CTTATAAATTTATAAG in a host-guest complex Deposited 2015-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 683–937（255 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 4000	Resolution 1.68 Å R-free 0.241
4XPE Crystal structure of 5'-CTTATGGGCCCATAAG in a host-guest complex Deposited 2015-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 683–937（255 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 4000	Resolution 1.78 Å R-free 0.237
5DMQ Crystal structure of mouse eRF1 in complex with Reverse Transcriptase (RT) of Moloney Murine Leukemia Virus Deposited 2015-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 683–1330（648 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.02 M magnesium chloride, 0.1 M HEPES pH 7.5, 20 % polyacrylic acid sodium salt 5100	Resolution 4.00 Å R-free 0.295
5DMR Crystal Structure of C-terminal domain of mouse eRF1 in complex with RNase H domain of RT of Moloney Murine Leukemia Virus Deposited 2015-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1159–1330（172 aa） Fragment：RNase H domain, UNP residues 1159-1330	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；288 K；0.1 M Tris pH 8.5, 18 % ammonium dihydrogen phosphate	Resolution 2.80 Å R-free 0.280
5VBS Structural basis for a six letter alphabet including GATCKX Deposited 2017-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 683–937（255 aa） Fragment：unp residues 683-987	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；10 % PEG 4000, 5 mM magnesium acetate and 50 mM ADA (pH 6.5)	Resolution 1.75 Å R-free 0.238
6B1Q Hydrogen Bonding Complementary, not size complementarity is key in the formation of the double helix Deposited 2017-09-18	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: hexameric	Chain A 683–937（255 aa） Fragment：Catalytic fragment (UNP residues 683-937)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；6 % PEG 4000, 5 mM magnesium acetate and 50 mM ADA (pH 6.5)	Resolution 1.90 Å R-free 0.237
6B1R Hydrogen Bonding Complementary, not size complementarity is key in the formation of the double helix Deposited 2017-09-18	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: hexameric	Chain A 683–937（255 aa） Fragment：Catalytic fragment (UNP residues 683-937)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；6 % PEG 4000, 5 mM magnesium acetate and 50 mM ADA (pH 6.5)	Resolution 1.69 Å R-free 0.230
6B1S Hydrogen Bonding Complementary, not size complementarity is key in the formation of the double helix Deposited 2017-09-18	Different construct 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 683–937（255 aa） Fragment：Catalytic fragment (UNP residues 683-937) Chain B 683–937（255 aa） Fragment：Catalytic fragment (UNP residues 683-937)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；6 % PEG 4000, 5 mM magnesium acetate and 50 mM ADA (pH 6.5)	Resolution 2.00 Å R-free 0.251
6MIG Crystal structure of host-guest complex with PB hachimoji DNA Deposited 2018-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 683–937（255 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8 % PEG 4000, 5 mM magnesium acetate and 50 mM ADA (pH 6.5)	Resolution 1.70 Å R-free 0.256
6MIH Crystal structure of host-guest complex with PC hachimoji DNA Deposited 2018-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 683–937（255 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；8 % PEG 4000, 5 mM magnesium acetate and 50 mM ADA (pH 6.5)	Resolution 1.60 Å R-free 0.234
6MIK Crystal structure of host-guest complex with PP hachimoji DNA Deposited 2018-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 683–937（255 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；8 % PEG 4000, 5 mM magnesium acetate and 50 mM ADA (pH 6.5)	Resolution 1.70 Å R-free 0.247
7JQ8 Solution NMR structure of human Brd3 ET domain Deposited 2020-08-10	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 × 2 PDB declaration: dimeric	Chain B 1716–1738（23 aa） Fragment：C-terminal Tail, residues 1716-1738	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1 NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1 NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1 NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1 NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] MLV IN TP, 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] Brd3 ET, 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM Brd3 ET, 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM Brd3 ET, 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

44 other PDB entries and 44 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	POL_MLVMS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–100； UniProt 1338–1435 Author chain B； PDBConstruct 3–100； UniProt 1338–1435 Author chain C； PDBConstruct 3–100； UniProt 1338–1435 Author chain D； PDBConstruct 3–100； UniProt 1338–1435

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	4nzg
Deposition date deposition_date	2013-12-12
Structure title title	Crystal Structure of the N-terminal domain of Moloney murine leukemia virus integrase, Northeast Structural Genomics Consortium Target OR3
Keywords keywords	;Structural Genomics, PSI-Biology, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, RETROVIRAL INTEGRASE, ZN FINGER, VIRAL PROTEIN ;; VIRAL PROTEIN
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	25.20 Å
Radius of gyration Rg (electron density) rg_electron	25.28 Å
Forward intensity I(0) i0	34296000.00
Molecular weight molecular_weight	45674.0 kDa
Excluded volume excluded_volume	57412 Å³
Envelope volume envelope_volume	72286 Å³
Hydration-shell volume shell_volume	25229 Å³
Envelope diameter envelope_diameter	94.4 Å
Shell Rg shell_rg	31.36 Å
Envelope Rg envelope_rg	25.50 Å
Shape Rg shape_rg	25.44 Å
Total Rg total_rg	25.53 Å
Total atoms total_atoms	3176
Residues n_residues	372
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	84.8 Å
Rg (real space) rg_real	25.27 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	3.4300e+07
I(0) uncertainty (real space) i0_real_error	5.2220e+05
Rg (reciprocal space) rg_reciprocal	25.25 Å
I(0) (reciprocal space) i0_reciprocal	34300000.0000
Solution quality estimate total_estimate	0.8641
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.3 Å
Skewness Skewness skewness	0.474
Kurtosis Kurtosis kurtosis	-0.158
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5075000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.817; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.927; Smooth: 0.850

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Integrase p46
Molecular weight formula_weight	11751.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3243

SHTSEHFHYTVTDIKDLTKLGAIYDKTKKYWVYQGKPVMPDQFTFELLDFLHQLTHLSFSKMKALLERSHSPYYMLNRDRTLKNITETCKACAQVNASKS

来源 Source

来源生物 organism	Moloney murine leukemia virus
通用名 common_name	MoMLV
NCBI Class编号 ncbi_taxonomy_id	928306
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	2,3-DIHYDROXY-1,4-DITHIOBUTANE
Molecular weight formula_weight	154.3 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	52

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4nzgA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	4nzgB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	4nzgC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	4nzgD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily	70 —

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8. Citations (1)

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Unit-cell length a length_a	44.659 Å
Unit-cell length b length_b	38.440 Å
Unit-cell length c length_c	135.275 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.70 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.152 Å
Low-resolution limit resolution_low	45.072 Å
R factor r_factor	0.2359
R_work r_work	0.2344
R_free r_free	0.2654

fit	/app/data/saxs_computation/nz/4nzg/4nzg.fit
pddf	/app/data/pr_computation/nz/4nzg/4nzg.pr.out
profile	/app/data/saxs_computation/nz/4nzg/4nzg.dat