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- PDB-3o3w: Crystal Structure of BH2092 protein (residues 14-131) from Bacill... -

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Basic information

Entry
Database: PDB / ID: 3o3w
TitleCrystal Structure of BH2092 protein (residues 14-131) from Bacillus halodurans, Northeast Structural Genomics Consortium Target BhR228A
ComponentsBH2092 protein
KeywordsStructural Genomics / Unknown function / alpha-beta protein / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.91 Å
AuthorsForouhar, F. / Neely, H. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of BH2092 protein (residues 14-131) from Bacillus halodurans, Northeast Structural Genomics Consortium Target BhR228A
Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJul 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BH2092 protein
B: BH2092 protein
C: BH2092 protein
D: BH2092 protein
E: BH2092 protein
F: BH2092 protein
G: BH2092 protein
H: BH2092 protein
I: BH2092 protein


Theoretical massNumber of molelcules
Total (without water)129,5129
Polymers129,5129
Non-polymers00
Water1,42379
1
A: BH2092 protein
B: BH2092 protein
C: BH2092 protein


Theoretical massNumber of molelcules
Total (without water)43,1713
Polymers43,1713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-22 kcal/mol
Surface area17720 Å2
MethodPISA
2
D: BH2092 protein
E: BH2092 protein
F: BH2092 protein


Theoretical massNumber of molelcules
Total (without water)43,1713
Polymers43,1713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-23 kcal/mol
Surface area17510 Å2
MethodPISA
3
G: BH2092 protein
H: BH2092 protein
I: BH2092 protein


Theoretical massNumber of molelcules
Total (without water)43,1713
Polymers43,1713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-22 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.239, 114.239, 85.452
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
BH2092 protein


Mass: 14390.197 Da / Num. of mol.: 9 / Fragment: sequence database residues 14-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: BH2092 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q9KB42
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 277 K / pH: 5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 0.1M sodium acetate (pH 5), 20% PEG 400, and 0.1M KH2PO4, Microbatch, under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97899
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 23, 2010 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 54786 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 60.7 Å2 / Rmerge(I) obs: 0.166 / Rsym value: 0.174 / Net I/σ(I): 12.65
Reflection shellResolution: 2.9→3 Å / Redundancy: 4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.18 / Rsym value: 0.509 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
SCALEPACKdata scaling
SHELXFOLLOWED BY SOLVE/RESOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.91→19.79 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 274374 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.292 5097 9.9 %RANDOM
Rwork0.25 ---
obs0.25 51439 93.9 %-
all-54780 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.91 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2---0.73 Å20 Å2
3---1.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.91→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8274 0 0 79 8353
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.358 416 11.1 %
Rwork0.296 3322 -
obs--68.2 %

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