4j5k

Crystal structure analysis of Streptomyces aureofaciens ribonuclease Sa Y51F mutant

Method: X-RAY DIFFRACTION D_max: 76.9 Å Quality: REASONABLE

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

Guanyl-specific ribonuclease Sa

Streptomyces aureofaciens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–96	Fragment：Ribonuclease Sa Mutation：Y51F	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；Ammonium sulfate 0.9 M, phosphate buffer 0.1 M , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.23 Å R-free 0.136
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–96	Fragment：Ribonuclease Sa Mutation：Y51F	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；Ammonium sulfate 0.9 M, phosphate buffer 0.1 M , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.23 Å R-free 0.136
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–96 Chain B； UniProt 1–96	Fragment：Ribonuclease Sa Mutation：Y51F	SO4 SULFATE ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；Ammonium sulfate 0.9 M, phosphate buffer 0.1 M , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.23 Å R-free 0.136

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 4J5K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AY7 RIBONUCLEASE SA COMPLEX WITH BARSTAR Deposited 1997-11-14	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 1–96（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 1.70 Å R-free 0.190
1BOX N39S MUTANT OF RNASE SA FROM STREPTOMYCES AUREOFACIENS Deposited 1998-08-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–96（96 aa）	Mutation：N39S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；HANGING DROP VAPOUR EQUILIBRATION DROP: 10 MG/ML OF PROTEIN 0.1 M TRIS-HCL BUFFER AT PH 8.0 12,5 % PEG 6000 RESERVOIR: 25 % PEG 6000	Resolution 1.60 Å R-free 0.218
1C54 SOLUTION STRUCTURE OF RIBONUCLEASE SA Deposited 1999-10-22	Different construct Different mutation/modification 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 1–96（96 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；303.2 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT NMR measurement conditions pH 5.5；303.2 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT NMR measurement conditions pH 5.5；303.2 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT NMR measurement conditions pH 5.5；303.2 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT NMR sample composition NA NMR sample composition NA NMR sample composition U-15N NMR sample composition U-15N	Resolution not provided
1GMP COMPLEX OF RIBONUCLEASE FROM STREPTOMYCES AUREOFACIENS WITH 2'-GMP AT 1.7 ANGSTROMS RESOLUTION Deposited 1992-10-01	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 1–96（96 aa） Chain B 1–96（96 aa）	Not recorded	SO4 SULFATE ION × 1 2GP GUANOSINE-2'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å
1GMQ COMPLEX OF RIBONUCLEASE FROM STREPTOMYCES AUREOFACIENS WITH 2'-GMP AT 1.7 ANGSTROMS RESOLUTION Deposited 1992-10-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–96（96 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1GMQ COMPLEX OF RIBONUCLEASE FROM STREPTOMYCES AUREOFACIENS WITH 2'-GMP AT 1.7 ANGSTROMS RESOLUTION Deposited 1992-10-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–96（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1GMR COMPLEX OF RIBONUCLEASE FROM STREPTOMYCES AUREOFACIENS WITH 2'-GMP AT 1.7 ANGSTROMS RESOLUTION Deposited 1992-10-01	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 1–96（96 aa） Chain B 1–96（96 aa）	Not recorded	SO4 SULFATE ION × 1 2GP GUANOSINE-2'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.77 Å
1I70 CRYSTAL STRUCTURE OF RNASE SA Y86F MUTANT Deposited 2001-03-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–96（96 aa）	Mutation：Y86F	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；AMMONIUM SULFATE, MONOSODIUM PHOSPHATE, DISODIUM PHOSPHATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.178
1I70 CRYSTAL STRUCTURE OF RNASE SA Y86F MUTANT Deposited 2001-03-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–96（96 aa）	Mutation：Y86F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；AMMONIUM SULFATE, MONOSODIUM PHOSPHATE, DISODIUM PHOSPHATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.178
1I8V CRYSTAL STRUCTURE OF RNASE SA Y80F MUTANT Deposited 2001-03-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–96（96 aa）	Mutation：Y80F	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；AMMONIUM SULFATE, MONOSODIUM PHOSPHATE, DISODIUM PHOSPHATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.25 Å R-free 0.156
1I8V CRYSTAL STRUCTURE OF RNASE SA Y80F MUTANT Deposited 2001-03-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–96（96 aa）	Mutation：Y80F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；AMMONIUM SULFATE, MONOSODIUM PHOSPHATE, DISODIUM PHOSPHATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.25 Å R-free 0.156
1LNI CRYSTAL STRUCTURE ANALYSIS OF A RIBONUCLEASE FROM STREPTOMYCES AUREOFACIENS AT ATOMIC RESOLUTION (1.0 A) Deposited 2002-05-03	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–96（96 aa）	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；ammonium sulfate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.00 Å
1LNI CRYSTAL STRUCTURE ANALYSIS OF A RIBONUCLEASE FROM STREPTOMYCES AUREOFACIENS AT ATOMIC RESOLUTION (1.0 A) Deposited 2002-05-03	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–96（96 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；ammonium sulfate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.00 Å
1RGE HYDROLASE, GUANYLORIBONUCLEASE Deposited 1995-06-05	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 1–96（96 aa） Chain B 1–96（96 aa）	Not recorded	SO4 SULFATE ION × 1 2GP GUANOSINE-2'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.7；ROOM TEMPERATURE, PH 6.7, AMMONIUM SULFATE	Resolution 1.15 Å
1RGF HYDROLASE, GUANYLORIBONUCLEASE Deposited 1995-06-05	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 1–96（96 aa） Chain B 1–96（96 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.7；ROOM TEMPERATURE, PH 6.7, AMMONIUM SULFATE	Resolution 1.20 Å
1RGG HYDROLASE, GUANYLORIBONUCLEASE Deposited 1995-06-05	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 1–96（96 aa） Chain B 1–96（96 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.20 Å
1RGH HYDROLASE, GUANYLORIBONUCLEASE Deposited 1995-06-05	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 1–96（96 aa） Chain B 1–96（96 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.20 Å
1RSN RIBONUCLEASE (RNASE SA) (E.C.3.1.4.8) COMPLEXED WITH EXO-2',3'-CYCLOPHOSPHOROTHIOATE Deposited 1995-09-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–96（96 aa）	Not recorded	SO4 SULFATE ION × 1 SGP GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1RSN RIBONUCLEASE (RNASE SA) (E.C.3.1.4.8) COMPLEXED WITH EXO-2',3'-CYCLOPHOSPHOROTHIOATE Deposited 1995-09-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–96（96 aa）	Not recorded	SGP GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1SAR DETERMINATION AND RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURES OF RIBONUCLEASE SA AND ITS COMPLEX WITH 3'-GUANYLIC ACID AT 1.8 ANGSTROMS RESOLUTION Deposited 1990-12-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–96（96 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1SAR DETERMINATION AND RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURES OF RIBONUCLEASE SA AND ITS COMPLEX WITH 3'-GUANYLIC ACID AT 1.8 ANGSTROMS RESOLUTION Deposited 1990-12-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–96（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1T2H Y81W mutant of RNase Sa from Streptomyces aureofaciens Deposited 2004-04-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–96（96 aa）	Mutation：Y81W	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；ammonium sulfate, disodium phosphate, monosodium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.00 Å R-free 0.166
1T2H Y81W mutant of RNase Sa from Streptomyces aureofaciens Deposited 2004-04-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–96（96 aa）	Mutation：Y81W	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；295 K；ammonium sulfate, disodium phosphate, monosodium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.00 Å R-free 0.166
1T2I T76W mutant of RNase Sa from Streptomyces aureofaciens Deposited 2004-04-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–96（96 aa）	Mutation：T76W	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；ammonium sulfate, disodium phosphate, monosodium phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.10 Å R-free 0.167
1UCI Mutants of RNase Sa Deposited 2003-04-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–96（96 aa）	Mutation：V2T	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.6M ammonium sulfate, 0.1M MES pH 6.5, 10%(v/v) dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.208
1UCI Mutants of RNase Sa Deposited 2003-04-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–96（96 aa）	Mutation：V2T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.6M ammonium sulfate, 0.1M MES pH 6.5, 10%(v/v) dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.208
1UCJ Mutants of RNase Sa Deposited 2003-04-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–96（96 aa）	Mutation：V36T	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.6M ammonium sulfate, 0.1M MES pH 6.5, 10%(v/v) dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.81 Å R-free 0.227
1UCJ Mutants of RNase Sa Deposited 2003-04-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–96（96 aa）	Mutation：V36T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.6M ammonium sulfate, 0.1M MES pH 6.5, 10%(v/v) dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.81 Å R-free 0.227
1UCK Mutants of RNase Sa Deposited 2003-04-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–96（96 aa）	Mutation：V43T	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.6M ammonium sulfate, 0.1M MES pH 6.5, 10%(v/v) dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.214
1UCK Mutants of RNase Sa Deposited 2003-04-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–96（96 aa）	Mutation：V43T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.6M ammonium sulfate, 0.1M MES pH 6.5, 10%(v/v) dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.214
1UCL Mutants of RNase Sa Deposited 2003-04-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–96（96 aa）	Mutation：V57T	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；293 K；2.0M ammonium sulfate, 0.1M HEPES-Na pH 7.5, 2%(v/v) PEG400, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.82 Å R-free 0.218
1UCL Mutants of RNase Sa Deposited 2003-04-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–96（96 aa）	Mutation：V57T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；293 K；2.0M ammonium sulfate, 0.1M HEPES-Na pH 7.5, 2%(v/v) PEG400, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.82 Å R-free 0.218
1YNV Asp79 makes a large, unfavorable contribution to the stability of RNase Sa Deposited 2005-01-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–96（96 aa）	Mutation：Q94K	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 10.5；291 K；1.2 M NaH2PO4/0.8M K2HPO4, 0.1 M CAPS, pH 10.5 and 0.2 M Li2SO4., EVAPORATION, temperature 291K	Resolution 1.20 Å R-free 0.178
1ZGX Crystal structure of ribonuclease mutant Deposited 2005-04-22	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 1–63（63 aa） Fragment：residues 1-63 Chain B 64–96（33 aa） Fragment：residues 64-96	Mutation：Q94K	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；ammonium sulfate, Hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.13 Å R-free 0.164
2SAR DETERMINATION AND RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURES OF RIBONUCLEASE SA AND ITS COMPLEX WITH 3'-GUANYLIC ACID AT 1.8 ANGSTROMS RESOLUTION Deposited 1990-12-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–96（96 aa）	Not recorded	SO4 SULFATE ION × 1 3GP GUANOSINE-3'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
2SAR DETERMINATION AND RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURES OF RIBONUCLEASE SA AND ITS COMPLEX WITH 3'-GUANYLIC ACID AT 1.8 ANGSTROMS RESOLUTION Deposited 1990-12-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–96（96 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
3A5E Crystal structure of 5K RNase Sa Deposited 2009-08-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–96（96 aa）	Mutation：D1K, D17K, D25K, E41K, E74K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；30% PEG4000, 200mM NaAcetate, 100mM Tris pH8.5, pH4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.281
4GHO Crystal Structure Analysis of Streptomyces aureofaciens Ribonuclease S24A mutant Deposited 2012-08-08	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 1–96（96 aa） Chain B 1–96（96 aa）	Mutation：S24A Mutation：S24A	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；0.7M ammonium sulfate, phosphate buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298, temperature 298.0K	Resolution 1.10 Å R-free 0.117
4J5G Crystal structure analysis of Streptomyces aureofaciens ribonuclease Sa T95A mutant Deposited 2013-02-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–96（96 aa）	Mutation：T95A	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；ammonium sulfate 0.8 M, cacodylate buffer 0.1M , pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.31 Å R-free 0.150
4J5G Crystal structure analysis of Streptomyces aureofaciens ribonuclease Sa T95A mutant Deposited 2013-02-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–96（96 aa）	Mutation：T95A	GOL GLYCEROL × 1 CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；ammonium sulfate 0.8 M, cacodylate buffer 0.1M , pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.31 Å R-free 0.150
4J5G Crystal structure analysis of Streptomyces aureofaciens ribonuclease Sa T95A mutant Deposited 2013-02-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–96（96 aa） Chain B 1–96（96 aa）	Mutation：T95A Mutation：T95A	SO4 SULFATE ION × 3 GOL GLYCEROL × 1 CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；ammonium sulfate 0.8 M, cacodylate buffer 0.1M , pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.31 Å R-free 0.150

27 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RNSA_STRAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–96； UniProt 1–96 Author chain B； PDBConstruct 1–96； UniProt 1–96

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	4j5k
Deposition date deposition_date	2013-02-08
Structure title title	Crystal structure analysis of Streptomyces aureofaciens ribonuclease Sa Y51F mutant
Keywords keywords	hydrolase, endoribonuclease, mutant; HYDROLASE
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	21.27 Å
Radius of gyration Rg (electron density) rg_electron	20.71 Å
Forward intensity I(0) i0	8938950.00
Molecular weight molecular_weight	21385.0 kDa
Excluded volume excluded_volume	26338 Å³
Envelope volume envelope_volume	32204 Å³
Hydration-shell volume shell_volume	14230 Å³
Envelope diameter envelope_diameter	69.8 Å
Shell Rg shell_rg	24.90 Å
Envelope Rg envelope_rg	20.77 Å
Shape Rg shape_rg	20.66 Å
Total Rg total_rg	21.45 Å
Total atoms total_atoms	1507
Residues n_residues	192
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	76.9 Å
Rg (real space) rg_real	21.44 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	8.9390e+06
I(0) uncertainty (real space) i0_real_error	1.2600e+05
Rg (reciprocal space) rg_reciprocal	21.41 Å
I(0) (reciprocal space) i0_reciprocal	8939000.0000
Solution quality estimate total_estimate	0.6963
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.2 Å
Skewness Skewness skewness	0.457
Kurtosis Kurtosis kurtosis	-0.560
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3550000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.520; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.489; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Guanyl-specific ribonuclease Sa
Molecular weight formula_weight	10566.5 kDa
EC 编号 ec_number	3.1.27.3
Mutation mutation	Y51F
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2099

DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGFYHEYTVITPGARTRGTRRIITGEATQEDYYTGDHYATFSLIDQTC

来源 Source

来源生物 organism	Streptomyces aureofaciens
NCBI Class编号 ncbi_taxonomy_id	1894
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	416

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4j5ka_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.1 — Microbial ribonucleases
Superfamily Superfamily superfamily	d.1.1 — Microbial ribonucleases
Family Family family	d.1.1.2 — Bacterial ribonucleases

Domain ID domain_id	d4j5kb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.1 — Microbial ribonucleases
Superfamily Superfamily superfamily	d.1.1 — Microbial ribonucleases
Family Family family	d.1.1.2 — Bacterial ribonucleases

CATH v4.4 (2 domains)

Domain ID domain_id	4j5kA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	30 — Microbial ribonucleases

Domain ID domain_id	4j5kB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	30 — Microbial ribonucleases

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8. Citations (1)

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Unit-cell length a length_a	38.303 Å
Unit-cell length b length_b	63.813 Å
Unit-cell length c length_c	77.624 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.230 Å
Low-resolution limit resolution_low	18.590 Å
R factor r_factor	0.1057
R_work r_work	0.1040
R_free r_free	0.1357

fit	/app/data/saxs_computation/j5/4j5k/4j5k.fit
pddf	/app/data/pr_computation/j5/4j5k/4j5k.pr.out
profile	/app/data/saxs_computation/j5/4j5k/4j5k.dat