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- PDB-1njh: Crystal Structure of Bacillus subtilis YojF protein -

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Basic information

Entry
Database: PDB / ID: 1njh
TitleCrystal Structure of Bacillus subtilis YojF protein
Componentsprotein yojF
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / YojF / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyHypothetical protein YojF / Protein of unknown function DUF1806 / Hypothetical protein YojF superfamily / Protein of unknown function (DUF1806) / Protein Yojf; Chain: A; / Distorted Sandwich / Mainly Beta / ISOPROPYL ALCOHOL / Uncharacterized protein YojF
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsKim, Y. / Korolev, O. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Bacillus subtilis YojF protein
Authors: Kim, Y. / Korolev, O. / Joachimiak, A.
History
DepositionDec 31, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: protein yojF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6253
Polymers13,4731
Non-polymers1522
Water1,60389
1
A: protein yojF
hetero molecules

A: protein yojF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2506
Polymers26,9462
Non-polymers3044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+11
MethodPQS
2


  • Idetical with deposited unit in distinct coordinate
  • defined by software
TypeNameSymmetry operationNumber
crystal symmetry operation1_554x,y,z-11
MethodPISA
Unit cell
Length a, b, c (Å)78.703, 78.703, 31.074
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

21A-207-

HOH

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Components

#1: Protein protein yojF


Mass: 13472.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YojF / Production host: Escherichia coli (E. coli) / References: UniProt: O31858
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Isopropanol, Sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97921
SYNCHROTRONAPS 19-ID20.97915, 0.97926, 0.94644
Detector
TypeIDDetectorDateDetails
SBC-21CCDAug 18, 2002mirror
SBC-22CCDSep 1, 2002mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2double crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979211
20.979151
30.979261
40.946441
ReflectionResolution: 1.7→28.27 Å / Num. all: 12326 / Num. obs: 12326 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 9.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1220 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
d*TREKdata reduction
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→28.28 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The number of reflections for refinement is greater than the number of reflections for data collection, because in CNS (hlml taget) refinement, the Friedel's pair was treated as two seperated reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1215 10.3 %RANDOM
Rwork0.22 ---
all0.223 22615 --
obs0.223 22615 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.6261 Å2 / ksol: 0.402038 e/Å3
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.73 Å20 Å2
2---0.22 Å20 Å2
3---0.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.7→28.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms851 0 10 89 950
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.41.5
X-RAY DIFFRACTIONc_mcangle_it3.762
X-RAY DIFFRACTIONc_scbond_it3.312
X-RAY DIFFRACTIONc_scangle_it5.132.5
LS refinement shellResolution: 1.7→1.77 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 221 9.5 %
Rwork0.281 1655 -
obs-2264 88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ISP.PARAMISP.TOP
X-RAY DIFFRACTION4GOL.PARAMGOL.TOP

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