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- PDB-1b3s: STRUCTURAL RESPONSE TO MUTATION AT A PROTEIN-PROTEIN INTERFACE -

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Basic information

Entry
Database: PDB / ID: 1b3s
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 / OTHER / Resolution: 2.39 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
DepositionDec 1, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Dec 9, 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: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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)


Theoretical massNumber of molelcules
Total (without water)68,0056
Polymers68,0056
Non-polymers00
Water3,711206
1
A: PROTEIN (BARNASE)
D: PROTEIN (BARSTAR)


Theoretical massNumber of molelcules
Total (without water)22,6682
Polymers22,6682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (BARNASE)
E: PROTEIN (BARSTAR)


Theoretical massNumber of molelcules
Total (without water)22,6682
Polymers22,6682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (BARNASE)
F: PROTEIN (BARSTAR)


Theoretical massNumber of molelcules
Total (without water)22,6682
Polymers22,6682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)201.900, 43.900, 83.400
Angle α, β, γ (deg.)90.00, 110.70, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.246804, -0.892861, 0.376678), (-0.893682, 0.0594, -0.444752), (0.374727, -0.446397, -0.812594)36.4197, 45.082, 35.8415
2given(0.579357, -0.052606, 0.813375), (-0.089693, -0.995969, -0.000528), (0.810124, -0.072648, -0.58174)-17.2022, 86.2812, 23.4397
3given(-0.235923, -0.875786, 0.421117), (-0.886622, 0.016596, -0.462197), (0.397797, -0.482415, -0.780406)35.7605, 46.6111, 35.4965
4given(0.60643, -0.023356, 0.794794), (-0.035467, -0.999368, -0.002306), (0.794345, -0.026791, -0.606875)-19.3469, 83.4461, 25.0618

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Components

#1: Protein PROTEIN (BARNASE)


Mass: 12331.651 Da / Num. of mol.: 3 / Mutation: H102A
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: 10336.739 Da / Num. of mol.: 3 / Mutation: Y30F
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTER SER: THE ORIGINAL SEQUENCE OF BARSTAR OMITTED AN N-TERMINAL METHIONINE, WHICH WAS VISIBLE IN ...TER SER: THE ORIGINAL SEQUENCE OF BARSTAR OMITTED AN N-TERMINAL METHIONINE, WHICH WAS VISIBLE IN THE ELECTRON DENSITY FOR THE D & E CHAINS. THE ORIGINAL SEQUENCE THEREFORE LISTS SER 89 AS THE C-TERMINUS. IN THIS STRUCTURE SER 90 IS THE C-TERMINAL RESIDUE

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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: 2.55 Å3/Da / Density % sol: 53 %
Description: RIGID-BODY REFINEMENT OF 1BRS WAS USED TO SOLVE THE STRUCTURE
Crystal growpH: 8 / Details: 0.2M (NH4)2SO4; 0.1M TRIS/HCL PH 8.0: 22% PEG-8000
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2TRIS_HCL11
3NH4 SULFATE11
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118-24 %(w/v)PEG80001reservoir
20.2 Mammonium sulfate1reservoir
30.1 MTris1reservoir
420 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.391→38.925 Å / Num. obs: 26773 / % possible obs: 96.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.42
Reflection shellResolution: 2.39→2.52 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 2.51 / % possible all: 90
Reflection shell
*PLUS
% possible obs: 90 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1BRS

1brs


Resolution: 2.39→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.324 -5 %
Rwork0.247 --
obs-25161 9.62 %
Displacement parametersBiso mean: 34 Å2
Refinement stepCycle: LAST / Resolution: 2.39→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4686 0 0 206 4892
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0060.02
X-RAY DIFFRACTIONp_angle_d0.0230.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0210.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8392
X-RAY DIFFRACTIONp_mcangle_it1.5153
X-RAY DIFFRACTIONp_scbond_it0.7312
X-RAY DIFFRACTIONp_scangle_it1.2383
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.0870.15
X-RAY DIFFRACTIONp_singtor_nbd0.1830.3
X-RAY DIFFRACTIONp_multtor_nbd0.2340.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1550.3
X-RAY DIFFRACTIONp_planar_tor2.97
X-RAY DIFFRACTIONp_staggered_tor1615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor2620
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_mcbond_it2
X-RAY DIFFRACTIONp_scbond_it2
X-RAY DIFFRACTIONp_mcangle_it3
X-RAY DIFFRACTIONp_scangle_it3

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