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- PDB-1b2s: STRUCTURAL RESPONSE TO MUTATION AT A PROTEIN-PROTEIN INTERFACE -

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Basic information

Entry
Database: PDB / ID: 1b2s
TitleSTRUCTURAL RESPONSE TO MUTATION AT A PROTEIN-PROTEIN INTERFACE
Components
  • PROTEIN (BARNASE)
  • PROTEIN (BARSTAR)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / RNASE-INHIBITOR COMPLEX / INTERFACIAL DOUBLE MUTANT / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region / cytoplasm
Similarity search - Function
Barstar-like / Barstar (barnase inhibitor) / Barstar (barnase inhibitor) / Barstar-like superfamily / Barnase; Chain D / : / Barnase / Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin ...Barstar-like / Barstar (barnase inhibitor) / Barstar (barnase inhibitor) / Barstar-like superfamily / Barnase; Chain D / : / Barnase / 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
Ribonuclease / Barstar
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsVaughan, C.K. / Buckle, A.M. / Fersht, A.R.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Structural response to mutation at a protein-protein interface.
Authors: Vaughan, C.K. / Buckle, A.M. / Fersht, A.R.
#1: Journal: Biochemistry / Year: 1994
Title: Protein-Protein Recognition: Crystal Structural Analysis of a Barnase-Barstar Complex at 2.0-A Resolution
Authors: Buckle, A.M. / Schreiber, G. / Fersht, A.R.
#2: Journal: Structure / Year: 1994
Title: Stability and Function: Two Constraints in the Evolution of Barstar and Other Proteins
Authors: Schreiber, G. / Buckle, A.M. / Fersht, A.R.
#3: Journal: Structure / Year: 1993
Title: Recognition between a Bacterial Ribonuclease, Barnase, and its Natural Inhibitor, Barstar
Authors: Guillet, V. / Lapthorn, A. / Hartley, R.W. / Mauguen, Y.
#4: Journal: Biochemistry / Year: 1993
Title: Interaction of Barnase with its Polypeptide Inhibitor Barstar Studied by Protein Engineering
Authors: Schreiber, G. / Fersht, A.R.
#5: Journal: Nature / Year: 1982
Title: Molecular Structures of a New Family of Ribonucleases
Authors: Mauguen, Y. / Hartley, R.W. / Dodson, E.J. / Dodson, G.G. / Bricogne, G. / Chothia, C. / Jack, A.
History
DepositionNov 30, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Dec 8, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (BARNASE)
B: PROTEIN (BARNASE)
C: PROTEIN (BARNASE)
D: PROTEIN (BARSTAR)
E: PROTEIN (BARSTAR)
F: PROTEIN (BARSTAR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1828
Polymers67,9906
Non-polymers1922
Water10,485582
1
A: PROTEIN (BARNASE)
D: PROTEIN (BARSTAR)


Theoretical massNumber of molelcules
Total (without water)22,6632
Polymers22,6632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (BARNASE)
E: PROTEIN (BARSTAR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8554
Polymers22,6632
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (BARNASE)
F: PROTEIN (BARSTAR)


Theoretical massNumber of molelcules
Total (without water)22,6632
Polymers22,6632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)206.240, 43.510, 83.690
Angle α, β, γ (deg.)90.00, 107.42, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.222582, -0.907497, 0.356239), (-0.88726, 0.037135, -0.459771), (0.404013, -0.418413, -0.813452)39.8215, 49.259, 37.3714
2given(0.682305, 0.029232, 0.730483), (-0.027492, -0.997467, 0.065595), (0.73055, -0.064838, -0.679774)-21.5404, 92.8856, 23.4131
3given(-0.186961, -0.902901, 0.38706), (-0.888914, -0.012234, -0.45791), (0.418183, -0.429674, -0.800314)39.6169, 50.4526, 37.0396
4given(0.620576, 0.002498, 0.784142), (-0.004879, -0.999963, 0.007047), (0.784131, -0.008199, -0.620541)-24.4649, 89.8795, 22.6121

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Components

#1: Protein PROTEIN (BARNASE)


Mass: 12340.618 Da / Num. of mol.: 3 / Mutation: K27A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Cellular location: EXTRACELLULAR / Plasmid: PMT410 / Production host: Escherichia coli (E. coli) / Strain (production host): TG2 / References: UniProt: P00648, EC: 3.1.27.3
#2: Protein PROTEIN (BARSTAR)


Mass: 10322.713 Da / Num. of mol.: 3 / Mutation: T43A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Cellular location: CYTOSOL / Plasmid: PML2BS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)[PLYSE] / References: UniProt: P11540
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growpH: 8 / Details: 18% PEG-4K 0.1M TRIS PH8.0 0.2M LI2SO4
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2TRIS11
3LI SULFATE11
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120-24 %(w/v)PEG40001reservoir
20.2 M1reservoirLiSO4
30.1 MTris1reservoir
420 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.911
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.911 Å / Relative weight: 1
ReflectionResolution: 1.82→33.71 Å / Num. obs: 59006 / % possible obs: 91.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 7.2
Reflection shellResolution: 1.82→1.91 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 3.2 / % possible all: 80.9
Reflection shell
*PLUS
% possible obs: 80.9 % / Mean I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BRS

1brs


Resolution: 1.82→31 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.249 -5 %
Rwork0.194 --
obs-64130 91.5 %
Displacement parametersBiso mean: 22.52 Å2
Refinement stepCycle: LAST / Resolution: 1.82→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4786 0 10 582 5378
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0280.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.030.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.442
X-RAY DIFFRACTIONp_mcangle_it2.123
X-RAY DIFFRACTIONp_scbond_it1.82
X-RAY DIFFRACTIONp_scangle_it2.653
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1210.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.2450.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.130.3
X-RAY DIFFRACTIONp_planar_tor4.17
X-RAY DIFFRACTIONp_staggered_tor14.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.720
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 31 Å / Num. reflection obs: 55983 / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.193 / Rfactor Rfree: 0.248
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.83 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_mcbond_it21.44
X-RAY DIFFRACTIONp_scbond_it21.8
X-RAY DIFFRACTIONp_mcangle_it32.12
X-RAY DIFFRACTIONp_scangle_it32.65

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