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- PDB-1yvs: Trimeric domain swapped barnase -

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Basic information

Entry
Database: PDB / ID: 1yvs
TitleTrimeric domain swapped barnase
ComponentsBARNASE
KeywordsENDONUCLEASE / RIBONUCLEASE / DOMAIN SWAPPED / TRIMER
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZegers, I. / Wyns, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Trimeric domain-swapped barnase.
Authors: Zegers, I. / Deswarte, J. / Wyns, L.
History
DepositionDec 10, 1998Processing site: BNL
Revision 1.0Feb 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BARNASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5913
Polymers12,3991
Non-polymers1922
Water1,838102
1
A: BARNASE
hetero molecules

A: BARNASE
hetero molecules

A: BARNASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7739
Polymers37,1963
Non-polymers5766
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8950 Å2
ΔGint-97 kcal/mol
Surface area16830 Å2
MethodPISA
2
A: BARNASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)75,54518
Polymers74,3926
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)70.080, 70.080, 162.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-111-

SO4

21A-111-

SO4

31A-157-

HOH

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Components

#1: Protein BARNASE


Mass: 12398.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P00648, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mM1dropNaOAc
32 mMexo-guanosine 2',3'-phosphorothioate1drop
430 %(w/v)PEG60001reservoir
50.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1996 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.2→19.9 Å / % possible obs: 98 % / Redundancy: 22 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.069 / Net I/σ(I): 17
Reflection shellResolution: 2.17→2.23 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.158 / % possible all: 95
Reflection
*PLUS
Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 95 % / Rmerge(I) obs: 0.158

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BRN

1brn


Resolution: 2.2→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: INITIAL POSITIONAL AND B-FACTOR REFINEMENT WAS CARRIED OUT WITH X-PLOR (BRUNGER, 1992) FOR DATA IN THE RESOLUTION RANGE 7.0 - 1.5 ANGSTROMS. AT R-VALUES OF R=0.174 FOR |F| GREATER THAN 3 ...Details: INITIAL POSITIONAL AND B-FACTOR REFINEMENT WAS CARRIED OUT WITH X-PLOR (BRUNGER, 1992) FOR DATA IN THE RESOLUTION RANGE 7.0 - 1.5 ANGSTROMS. AT R-VALUES OF R=0.174 FOR |F| GREATER THAN 3 SIGMA(F), THE REFINEMENT WAS CONTINUED WITH THE PROGRAM SHELXL-93. THE FREE R VALUE WAS MONITORED IN THE FIRST STEPS OF REFINEMENT. THE MODEL WAS FINALLY REFINED USING ALL DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 625 10 %RANDOM
Rwork0.187 ---
obs0.187 7960 98.7 %-
Displacement parametersBiso mean: 29.61 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms864 0 10 102 976
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.502
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.49
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.229
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.308 78 7.4 %
Rwork0.238 786 -
obs--96.5 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.49
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.229
LS refinement shell
*PLUS
Rfactor obs: 0.238

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