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- PDB-1bns: STRUCTURAL STUDIES OF BARNASE MUTANTS -

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Basic information

Entry
Database: PDB / ID: 1bns
TitleSTRUCTURAL STUDIES OF BARNASE MUTANTS
ComponentsBARNASE
KeywordsENDONUCLEASE
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region
Similarity search - Function
: / Barnase / Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.05 Å
AuthorsChen, Y.W.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Contribution of buried hydrogen bonds to protein stability. The crystal structures of two barnase mutants.
Authors: Chen, Y.W. / Fersht, A.R. / Henrick, K.
#1: Journal: Nature / Year: 1989
Title: Capping and Alpha-Helix Stability
Authors: Serrano, L. / Fersht, A.R.
#2: 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
DepositionApr 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)37,1063
Polymers37,1063
Non-polymers00
Water4,035224
1
A: BARNASE


Theoretical massNumber of molelcules
Total (without water)12,3691
Polymers12,3691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BARNASE


Theoretical massNumber of molelcules
Total (without water)12,3691
Polymers12,3691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BARNASE


Theoretical massNumber of molelcules
Total (without water)12,3691
Polymers12,3691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.370, 59.370, 82.166
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Atom site foot note1: RESIDUE HIS B 102 HAS ALTERNATE CONFORMATIONS FOR ITS SIDE CHAINS.

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Components

#1: Protein BARNASE


Mass: 12368.694 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria)
References: UniProt: P00648, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.25 Å3/Da / Density % sol: 45.4 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 41566 / % possible obs: 75 % / Num. measured all: 93923 / Rmerge(I) obs: 0.039

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.05→6 Å / σ(F): 3 /
RfactorNum. reflection
obs0.169 17605
Refinement stepCycle: LAST / Resolution: 2.05→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2553 0 0 224 2777
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0520.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0580.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.471.5
X-RAY DIFFRACTIONp_mcangle_it2.392
X-RAY DIFFRACTIONp_scbond_it2.532
X-RAY DIFFRACTIONp_scangle_it3.823
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.1380.12
X-RAY DIFFRACTIONp_singtor_nbd0.1870.2
X-RAY DIFFRACTIONp_multtor_nbd0.1880.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1980.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.633
X-RAY DIFFRACTIONp_staggered_tor19.3320
X-RAY DIFFRACTIONp_orthonormal_tor2015
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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