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- PDB-1brs: PROTEIN-PROTEIN RECOGNITION: CRYSTAL STRUCTURAL ANALYSIS OF A BAR... -

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Basic information

Entry
Database: PDB / ID: 1brs
TitlePROTEIN-PROTEIN RECOGNITION: CRYSTAL STRUCTURAL ANALYSIS OF A BARNASE-BARSTAR COMPLEX AT 2.0-A RESOLUTION
Components
  • BARNASE
  • BARSTAR
KeywordsENDONUCLEASE
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 / Guanine-specific ribonuclease N1/T1/U2 / ribonuclease / Microbial ribonucleases ...Barstar-like / Barstar (barnase inhibitor) / Barstar (barnase inhibitor) / Barstar-like superfamily / Barnase; Chain D / : / Barnase / Guanine-specific ribonuclease N1/T1/U2 / ribonuclease / Microbial ribonucleases / Ribonuclease/ribotoxin / 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 / Resolution: 2 Å
AuthorsBuckle, A.M. / Schreiber, G. / Fersht, A.R.
Citation
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.
#1: 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.
#2: 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.
#3: Journal: Biochemistry / Year: 1993
Title: Interaction of Barnase with its Polypeptide Inhibitor Barstar Studied by Protein Engineering
Authors: Schreiber, G. / Fersht, A.R.
#4: 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
DepositionMar 11, 1994Processing site: BNL
Revision 1.0Jun 22, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Remark 700SHEET IN *SHEET* AND *TURN* RECORDS BELOW, *BN* REFERS TO BARNASE AND *BS* REFERS TO BARSTAR.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BARNASE
B: BARNASE
C: BARNASE
D: BARSTAR
E: BARSTAR
F: BARSTAR


Theoretical massNumber of molelcules
Total (without water)67,6686
Polymers67,6686
Non-polymers00
Water9,242513
1
A: BARNASE
D: BARSTAR


Theoretical massNumber of molelcules
Total (without water)22,5562
Polymers22,5562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BARNASE
E: BARSTAR


Theoretical massNumber of molelcules
Total (without water)22,5562
Polymers22,5562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BARNASE
F: BARSTAR


Theoretical massNumber of molelcules
Total (without water)22,5562
Polymers22,5562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)207.250, 43.860, 84.710
Angle α, β, γ (deg.)90.00, 107.76, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO D 48 / 2: CIS PROLINE - PRO E 48 / 3: CIS PROLINE - PRO F 48
Components on special symmetry positions
IDModelComponents
11B-183-

HOH

21B-192-

HOH

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Components

#1: Protein BARNASE


Mass: 12398.721 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(PLYSE) (PML2BS) CELLS
References: UniProt: P00648, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Protein BARSTAR


Mass: 10157.412 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(PLYSE) (PML2BS) CELLS / References: UniProt: P11540
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %PEG80001reservoir
2100 mMTris-HCl1reservoir
3100 mMammonium sulfate1reservoir
422 mg/mlprotein1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 43964 / % possible obs: 89.7 % / Observed criterion σ(F): 37.1 / Num. measured all: 142093 / Rmerge(I) obs: 0.09

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→7 Å / σ(F): 0 /
RfactorNum. reflection
obs0.172 43964
Refinement stepCycle: LAST / Resolution: 2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4640 0 0 513 5153
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0440.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0510.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.051.5
X-RAY DIFFRACTIONp_mcangle_it1.7382
X-RAY DIFFRACTIONp_scbond_it2.1172
X-RAY DIFFRACTIONp_scangle_it3.2663
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.1040.12
X-RAY DIFFRACTIONp_singtor_nbd0.2090.5
X-RAY DIFFRACTIONp_multtor_nbd0.2160.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.230.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.0683
X-RAY DIFFRACTIONp_staggered_tor17.40620
X-RAY DIFFRACTIONp_orthonormal_tor26.83315
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS

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