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- PDB-2cx6: Crystal structure of ribonuclease inhibitor Barstar -

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Basic information

Entry
Database: PDB / ID: 2cx6
TitleCrystal structure of ribonuclease inhibitor Barstar
ComponentsHypothetical protein yhcO
KeywordsHYDROLASE INHIBITOR / Barstar / ribonuclease inhibitor / RSGI / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative
Function / homologyBarstar-like / Barstar (barnase inhibitor) / Barstar (barnase inhibitor) / Barstar-like superfamily / Barnase; Chain D / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein YhcO
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.43 Å
AuthorsMurayama, K. / Kawazoe, M. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of ribonuclease inhibitor Barstar
Authors: Murayama, K. / Kawazoe, M. / Shirouzu, M. / Yokoyama, S.
History
DepositionJun 28, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein yhcO
B: Hypothetical protein yhcO


Theoretical massNumber of molelcules
Total (without water)21,8062
Polymers21,8062
Non-polymers00
Water61334
1
A: Hypothetical protein yhcO


Theoretical massNumber of molelcules
Total (without water)10,9031
Polymers10,9031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein yhcO


Theoretical massNumber of molelcules
Total (without water)10,9031
Polymers10,9031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.064, 51.064, 180.042
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Hypothetical protein yhcO / nuclease inhibitor


Mass: 10902.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: yhcO / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P64618
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.7M Sodium formate, 0.1M Sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9792, 0.9795, 0.964
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 24, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97951
30.9641
ReflectionResolution: 2.43→50 Å / Num. obs: 9619 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 29.4 Å2 / Rsym value: 0.062 / Net I/σ(I): 27.7
Reflection shellResolution: 2.43→2.52 Å / Rsym value: 0.232 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.43→49.13 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1287230.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.295 991 10.3 %RANDOM
Rwork0.229 ---
obs0.229 9593 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.8107 Å2 / ksol: 0.362069 e/Å3
Displacement parametersBiso mean: 45.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.2 Å20 Å20 Å2
2--4.2 Å20 Å2
3----8.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.43→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1528 0 0 34 1562
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it5.311.5
X-RAY DIFFRACTIONc_mcangle_it7.112
X-RAY DIFFRACTIONc_scbond_it8.612
X-RAY DIFFRACTIONc_scangle_it10.652.5
LS refinement shellResolution: 2.43→2.58 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.429 147 9.7 %
Rwork0.29 1370 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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