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- PDB-1ban: THE CONTRIBUTION OF BURIED HYDROGEN BONDS TO PROTEIN STABILITY: T... -

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Basic information

Entry
Database: PDB / ID: 1ban
TitleTHE CONTRIBUTION OF BURIED HYDROGEN BONDS TO PROTEIN STABILITY: THE CRYSTAL STRUCTURES OF TWO 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: 2.2 Å
AuthorsChen, Y.W. / Fersht, A.R. / Henrick, K.
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: J.Mol.Biol. / Year: 1992
Title: The Folding of an Enzyme. II. Substructure of Barnase and the Contribution of Different Interactions to Protein Stability
Authors: Serrano, L. / Kellis Junior, J.T. / Cann, P. / Matouschek, A. / 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
DepositionMay 19, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: 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

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Assembly

Deposited unit
A: BARNASE
B: BARNASE
C: BARNASE


Theoretical massNumber of molelcules
Total (without water)37,1483
Polymers37,1483
Non-polymers00
Water4,792266
1
A: BARNASE


Theoretical massNumber of molelcules
Total (without water)12,3831
Polymers12,3831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BARNASE


Theoretical massNumber of molelcules
Total (without water)12,3831
Polymers12,3831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BARNASE


Theoretical massNumber of molelcules
Total (without water)12,3831
Polymers12,3831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.527, 59.527, 82.652
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Atom site foot note1: WATERS A 6, A 11, A 19, A 21, A 41, A 64, A 69, B 60 AND C 92 ARE DISORDERED.

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Components

#1: Protein BARNASE


Mass: 12382.721 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.: 266 / 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: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
22.8 Mphosphate1reservoir
32 mM1reservoirZnSO4

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 6 Å / Num. obs: 16276 / % possible obs: 97.8 % / Num. measured all: 39235 / Rmerge(I) obs: 0.139

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→6 Å / σ(F): 3 /
RfactorNum. reflection
obs0.176 11821
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2559 0 0 266 2825
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.02
X-RAY DIFFRACTIONp_angle_d0.0590.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0590.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.361.5
X-RAY DIFFRACTIONp_mcangle_it2.132
X-RAY DIFFRACTIONp_scbond_it2.362
X-RAY DIFFRACTIONp_scangle_it3.383
X-RAY DIFFRACTIONp_plane_restr0.0170.02
X-RAY DIFFRACTIONp_chiral_restr0.1510.12
X-RAY DIFFRACTIONp_singtor_nbd0.1670.2
X-RAY DIFFRACTIONp_multtor_nbd0.1680.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.20.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.713
X-RAY DIFFRACTIONp_staggered_tor20.1720
X-RAY DIFFRACTIONp_orthonormal_tor20.9515
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Num. reflection all: 15464 / Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS

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