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- PDB-1s7h: Structural Genomics, 2.2A crystal structure of protein YKOF from ... -

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Basic information

Entry
Database: PDB / ID: 1s7h
TitleStructural Genomics, 2.2A crystal structure of protein YKOF from Bacillus subtilis
ComponentsykoF
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein YKOF / alpha-beta-beta-alpha sandwich / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Thiamin/hydroxymethyl pyrimidine-binding YkoF, putative / Hydroxymethyl pyrimidine (HMP)/thiamine binding protein / YKOF-related Family / Alpha-Beta Plaits - #930 / MTH1187/YkoF-like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative HMP/thiamine-binding protein YkoF
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsZhang, R. / Lezondra, L. / Moy, S. / Dementieva, I. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 2.2A crystal structure of protein YKOF from Bacillus subtilis
Authors: Zhang, R. / Lezondra, L. / Moy, S. / Dementieva, I. / Joachimiak, A.
History
DepositionJan 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ykoF
B: ykoF
C: ykoF
D: ykoF


Theoretical massNumber of molelcules
Total (without water)88,2074
Polymers88,2074
Non-polymers00
Water6,702372
1
A: ykoF
B: ykoF


Theoretical massNumber of molelcules
Total (without water)44,1042
Polymers44,1042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-24 kcal/mol
Surface area14400 Å2
MethodPISA
2
C: ykoF
D: ykoF


Theoretical massNumber of molelcules
Total (without water)44,1042
Polymers44,1042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-22 kcal/mol
Surface area14770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.740, 55.078, 85.493
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThis protein exists as dimer. Molecules A and B, C and D represents two dimers in asymmeiric unit

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Components

#1: Protein
ykoF


Mass: 22051.869 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: YKOF / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O34911
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.53 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M MgCl2 Hexahydrate, 0.1M Tris , 25% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795, 0.9798
DetectorType: SBC-2 / Detector: CCD / Date: Mar 10, 2003 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97981
ReflectionResolution: 2.2→50 Å / Num. obs: 81572 / % possible obs: 99 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 9.2 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 23.4
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.85 / Num. unique all: 2723 / % possible all: 95.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→46.2 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 320699.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Friedel's pairs were used in the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 3570 4.9 %RANDOM
Rwork0.221 ---
obs0.221 73081 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.8256 Å2 / ksol: 0.321195 e/Å3
Displacement parametersBiso mean: 35.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.44 Å20 Å20 Å2
2---2.35 Å20 Å2
3---4.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.2→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5643 0 0 372 6015
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.402 472 4.9 %
Rwork0.355 9099 -
obs--73.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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