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- PDB-1b2u: STRUCTURAL RESPONSE TO MUTATION AT A PROTEIN-PROTEIN INTERFACE -

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Basic information

Entry
Database: PDB / ID: 1b2u
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 / OTHER / Resolution: 2.1 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)67,9486
Polymers67,9486
Non-polymers00
Water7,422412
1
A: PROTEIN (BARNASE)
D: PROTEIN (BARSTAR)


Theoretical massNumber of molelcules
Total (without water)22,6492
Polymers22,6492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (BARNASE)
E: PROTEIN (BARSTAR)


Theoretical massNumber of molelcules
Total (without water)22,6492
Polymers22,6492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (BARNASE)
F: PROTEIN (BARSTAR)


Theoretical massNumber of molelcules
Total (without water)22,6492
Polymers22,6492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)201.230, 43.020, 83.470
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(-0.233861, -0.895035, 0.379763), (-0.888056, 0.037626, -0.458194), (0.39581, -0.444405, -0.803641)36.0077, 45.1773, 36.1357
2given(0.584385, -0.018297, 0.81127), (-0.04935, -0.998697, 0.013024), (0.809975, -0.047648, -0.584526)-18.7135, 84.339, 23.3416
3given(-0.222297, -0.878521, 0.42283), (-0.891225, 0.007242, -0.453504), (0.39535, -0.477649, -0.784569)36.0335, 46.4734, 35.508
4given(0.612388, -0.004396, 0.790545), (-0.022102, -0.999689, 0.011562), (0.790248, -0.024553, -0.612295)-19.5532, 83.2148, 25.0382

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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: 10308.729 Da / Num. of mol.: 3 / Mutation: D36A
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.: 412 / 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. 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: 2.49 Å3/Da / Density % sol: 51 %
Description: THE STRUCTURE WAS SOLVED BY RIGID BODY REFINEMENT OF PDB ENTRY 1BRS IN THE ASYMMETRIC UNIT
Crystal growpH: 6.5
Details: 21% PEG-8K 0.2 M AMMONIUM SULPHATE 0.1 M NA CACODYLATE PH6.5
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2NA CACODYLATE11
3NH4 SULFATE11
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
218-24 %(w/v)PEG80001reservoir
30.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1996 / Details: SUPER DOUBLE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→22.3 Å / Num. obs: 32841 / % possible obs: 98.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 24.56 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.45
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 4 / % possible all: 98.9
Reflection
*PLUS
Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 99.7 %

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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: 2.1→21.3 Å / SU B: 5.9 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.276 -5 %
Rwork0.214 --
obs-37091 98.9 %
Displacement parametersBiso mean: 29.17 Å2
Refinement stepCycle: LAST / Resolution: 2.1→21.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4698 0 0 413 5111
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.7212
X-RAY DIFFRACTIONp_mcangle_it2.6263
X-RAY DIFFRACTIONp_scbond_it1.8542
X-RAY DIFFRACTIONp_scangle_it2.7093
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1250.15
X-RAY DIFFRACTIONp_singtor_nbd0.1840.3
X-RAY DIFFRACTIONp_multtor_nbd0.2490.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1390.3
X-RAY DIFFRACTIONp_planar_tor4.17
X-RAY DIFFRACTIONp_staggered_tor16.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.820
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 21.3 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_mcbond_it2
X-RAY DIFFRACTIONp_scbond_it2
X-RAY DIFFRACTIONp_mcangle_it3
X-RAY DIFFRACTIONp_scangle_it3

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