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- PDB-1xjc: X-ray crystal structure of MobB protein homolog from Bacillus ste... -

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Basic information

Entry
Database: PDB / ID: 1xjc
TitleX-ray crystal structure of MobB protein homolog from Bacillus stearothermophilus
ComponentsMobB protein homolog
Keywordsstructural genomics / unknown function / MobB / Midwest Center for Structural Genomics / PSI / Protein Structure Initiative / MCSG
Function / homology
Function and homology information


Mo-molybdopterin cofactor biosynthetic process / GTP binding
Similarity search - Function
Molybdopterin-guanine dinucleotide biosynthesis protein B (MobB) domain / Molybdopterin guanine dinucleotide synthesis protein B / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MobB protein homolog
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsOsipiuk, J. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of MobB protein homolog from Bacillus stearothermophilus
Authors: Osipiuk, J. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionSep 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Sep 26, 2012Group: Structure summary
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.
Remark 999SEQUENCE THE SEQUENCE OF THE PROTEIN IS NOT YET AVAILABLE IN ANY REFERENCE SEQUENCE DATABASE. ...SEQUENCE THE SEQUENCE OF THE PROTEIN IS NOT YET AVAILABLE IN ANY REFERENCE SEQUENCE DATABASE. RESIDUES -2 TO 0 ARE CLONING ARTIFACTS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MobB protein homolog


Theoretical massNumber of molelcules
Total (without water)19,2251
Polymers19,2251
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: MobB protein homolog

A: MobB protein homolog


Theoretical massNumber of molelcules
Total (without water)38,4512
Polymers38,4512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3330 Å2
ΔGint-18 kcal/mol
Surface area14710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.889, 92.889, 39.107
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein MobB protein homolog


Mass: 19225.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: RBSTP0958 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3]pMAGIC / References: UniProt: D0VWV1*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.7 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: citric acid, sodium chloride, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979295 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 16, 2004
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979295 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 12603 / Num. obs: 11599 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.5 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 42.9
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 16.5 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 9.5 / Num. unique all: 753 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→30.41 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1472321.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 1132 9.8 %RANDOM
Rwork0.1955 ---
all0.1961 11568 --
obs0.1961 11568 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.2382 Å2 / ksol: 0.391931 e/Å3
Displacement parametersBiso mean: 29.5 Å2
Baniso -1Baniso -2Baniso -3
1-7.35 Å23.08 Å20 Å2
2--7.74 Å20 Å2
3----15.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.1→30.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1173 0 0 81 1254
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.442
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it3.32.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.228 174 9.2 %
Rwork0.204 1716 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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