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- PDB-1ay7: RIBONUCLEASE SA COMPLEX WITH BARSTAR -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1ay7
TitleRIBONUCLEASE SA COMPLEX WITH BARSTAR
Components
  • BARSTAR
  • GUANYL-SPECIFIC RIBONUCLEASE SA
KeywordsCOMPLEX (ENZYME/INHIBITOR) / RIBONUCLEASE / INHIBITOR / STREPTOMYCES AUREOFACIENS / COMPLEX (ENZYME-INHIBITOR) / COMPLEX (ENZYME-INHIBITOR) complex
Function / homology
Function and homology information


ribonuclease T1 / ribonuclease T1 activity / RNA endonuclease activity / lyase activity / RNA binding / extracellular region / cytoplasm
Similarity search - Function
Barstar-like / Barstar (barnase inhibitor) / Barstar (barnase inhibitor) / Barstar-like superfamily / Barnase; Chain D / Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / Nuclear Transport Factor 2; Chain: A, ...Barstar-like / Barstar (barnase inhibitor) / Barstar (barnase inhibitor) / Barstar-like superfamily / Barnase; Chain D / Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / Nuclear Transport Factor 2; Chain: A, / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Guanyl-specific ribonuclease Sa / Barstar
Similarity search - Component
Biological speciesStreptomyces aureofaciens (bacteria)
Bacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSevcik, J. / Urbanikova, L. / Dauter, Z. / Wilson, K.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Recognition of RNase Sa by the inhibitor barstar: structure of the complex at 1.7 A resolution.
Authors: Sevcik, J. / Urbanikova, L. / Dauter, Z. / Wilson, K.S.
History
DepositionNov 14, 1997Processing site: BNL
Revision 1.0Mar 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Data collection / Database references / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GUANYL-SPECIFIC RIBONUCLEASE SA
B: BARSTAR


Theoretical massNumber of molelcules
Total (without water)20,8042
Polymers20,8042
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.950, 56.950, 135.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein GUANYL-SPECIFIC RIBONUCLEASE SA


Mass: 10582.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Plasmid: PMT1126 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P05798, EC: 3.1.27.3
#2: Protein BARSTAR


Mass: 10221.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: BARNASE INHIBITOR / Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Plasmid: PMT1126 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P11540
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 69 %
Crystal growpH: 7 / Details: pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
20.1 Mcacodylate1drop
315 %ammonium sulfate1drop
430 %ammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. obs: 27413 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 27.3
Reflection shellResolution: 1.7→1.72 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.308 / % possible all: 99.8
Reflection
*PLUS
Num. all: 27413 / Num. obs: 22844 / Num. measured all: 118438

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BRS

1brs


Resolution: 1.7→25 Å / Cross valid method: FREE R / σ(F): 0
Details: ESTIMATED COORDINATE ERROR. ESD FROM CRUICKSHANK (A) : 0.078 ESD FROM SIGMAA (A) : 0.061
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2739 10 %RANDOM
Rwork0.16 ---
obs0.162 27352 100 %-
Displacement parametersBiso mean: 24.8 Å2
Baniso -1Baniso -2Baniso -3
1-23.8 Å23.5 Å20 Å2
2--23.8 Å20 Å2
3---21.8 Å2
Refine analyzeLuzzati sigma a obs: 0.06 Å
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 0 190 1678
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0250.02
X-RAY DIFFRACTIONp_angle_d0.040.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0890.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.93
X-RAY DIFFRACTIONp_mcangle_it4.25
X-RAY DIFFRACTIONp_scbond_it5.56
X-RAY DIFFRACTIONp_scangle_it7.48
X-RAY DIFFRACTIONp_plane_restr0.0350.04
X-RAY DIFFRACTIONp_chiral_restr0.2570.15
X-RAY DIFFRACTIONp_singtor_nbd0.1870.3
X-RAY DIFFRACTIONp_multtor_nbd0.2640.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1430.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1430.3
X-RAY DIFFRACTIONp_planar_tor12.87
X-RAY DIFFRACTIONp_staggered_tor1715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor23.520
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.19 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS

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