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- PDB-1kyh: Structure of Bacillus subtilis YxkO, a Member of the UPF0031 Fami... -

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Basic information

Entry
Database: PDB / ID: 1kyh
TitleStructure of Bacillus subtilis YxkO, a Member of the UPF0031 Family and a Putative Kinase
ComponentsHypothetical 29.9 kDa protein in SIGY-CYDD intergenic region
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


metabolite repair / ADP-dependent NAD(P)H-hydrate dehydratase / ADP-dependent NAD(P)H-hydrate dehydratase activity / NADHX epimerase activity / NADPHX epimerase activity / nicotinamide nucleotide metabolic process / ATP binding
Similarity search - Function
YjeF C-terminal domain signature 1. / Carbohydrate kinase, predicted, conserved site / YjeF C-terminal domain signature 2. / ATP/ADP-dependent (S)-NAD(P)H-hydrate dehydratase / Carbohydrate kinase / YjeF C-terminal domain profile. / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADP-dependent (S)-NAD(P)H-hydrate dehydratase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsZhang, R. / Dementieva, I. / Vinokour, E. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Struct.Biol. / Year: 2002
Title: Structure of Bacillus subtilis YXKO--a member of the UPF0031 family and a putative kinase.
Authors: Zhang, R. / Grembecka, J. / Vinokour, E. / Collart, F. / Dementieva, I. / Minor, W. / Joachimiak, A.
History
DepositionFeb 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical 29.9 kDa protein in SIGY-CYDD intergenic region


Theoretical massNumber of molelcules
Total (without water)30,1861
Polymers30,1861
Non-polymers00
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hypothetical 29.9 kDa protein in SIGY-CYDD intergenic region

A: Hypothetical 29.9 kDa protein in SIGY-CYDD intergenic region

A: Hypothetical 29.9 kDa protein in SIGY-CYDD intergenic region

A: Hypothetical 29.9 kDa protein in SIGY-CYDD intergenic region


Theoretical massNumber of molelcules
Total (without water)120,7424
Polymers120,7424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area9330 Å2
ΔGint-38 kcal/mol
Surface area37890 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.900, 91.900, 170.506
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
DetailsThis protein (APC234) existed as tetramer which is generated by the crystallographic four fold axis

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Components

#1: Protein Hypothetical 29.9 kDa protein in SIGY-CYDD intergenic region


Mass: 30185.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YXKO / Plasmid: MCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: P94368
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.98 Å3/Da / Density % sol: 58.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.15 M MgCl2, 28% PEG400, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mg/mlprotein1drop
228 %PEG4001reservoir
30.1 MHEPES1reservoirpH7.5
40.15 1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795,0.9798,0.94656
DetectorType: SBC-2 / Detector: CCD / Date: Nov 25, 2001 / 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
30.946561
ReflectionResolution: 1.6→50 Å / Num. obs: 92275 / % possible obs: 97.3 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 17 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 31
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 4.68 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2.09 / Num. unique all: 4902 / % possible all: 86
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 48555
Reflection shell
*PLUS
% possible obs: 86 % / Num. unique obs: 4216

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Processing

Software
NameClassification
d*TREKdata scaling
HKL-2000data reduction
CNSrefinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→33.3 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 950056.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: CNS library
Details: hlml refinement target of CNS was used in the refinement. The Friedel pairs were used in phasing and refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3754 4.9 %RANDOM
Rwork0.228 ---
all0.23 92275 --
obs0.229 76312 82.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.1038 Å2 / ksol: 0.424071 e/Å3
Displacement parametersBiso mean: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.57 Å20 Å20 Å2
2---2.57 Å20 Å2
3---5.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→33.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 0 209 2252
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it0.591.5
X-RAY DIFFRACTIONc_mcangle_it1.012
X-RAY DIFFRACTIONc_scbond_it0.982
X-RAY DIFFRACTIONc_scangle_it1.422.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 453 4.9 %
Rwork0.234 8786 -
obs--60.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 50 Å / Num. reflection obs: 48555
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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