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- PDB-1zc6: Crystal Structure of Putative N-acetylglucosamine Kinase from Chr... -

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Basic information

Entry
Database: PDB / ID: 1zc6
TitleCrystal Structure of Putative N-acetylglucosamine Kinase from Chromobacterium violaceum. Northeast Structural Genomics Target Cvr23.
Componentsprobable N-acetylglucosamine kinase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / N-acetylglucosamine kinase / NESG / Q7NU07_CHRVO / cvr23 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


N-acetylglucosamine kinase / N-acetylglucosamine kinase activity
Similarity search - Function
ATPase, BadF/BadG/BcrA/BcrD type / BadF/BadG/BcrA/BcrD ATPase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable N-acetylglucosamine kinase
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsVorobiev, S.M. / Kuzin, A. / Forouhar, F. / Abashidze, M. / Acton, T.B. / Xiao, R. / Ma, L.-C. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of Putative N-acetylglucosamine Kinase from Chromobacterium violaceum
Authors: Vorobiev, S.M. / Kuzin, A. / Forouhar, F. / Abashidze, M. / Acton, T.B. / Xiao, R. / Ma, L.-C. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionApr 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: probable N-acetylglucosamine kinase
B: probable N-acetylglucosamine kinase


Theoretical massNumber of molelcules
Total (without water)64,1202
Polymers64,1202
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)178.245, 178.245, 117.663
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein probable N-acetylglucosamine kinase


Mass: 32060.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Strain: ATCC 12472 / Gene: CV2896 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q7NU07
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 3.64 Å3/Da / Density % sol: 66.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.15-0.25 M magnesium chloride, 15-20% PEG 3350, 0.1 M MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9876 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9876 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 90884 / Num. obs: 90884 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.104
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.863 / % possible all: 95.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→29.42 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 291990.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 3353 3.9 %RANDOM
Rwork0.241 ---
obs0.241 85106 92.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.1422 Å2 / ksol: 0.340634 e/Å3
Displacement parametersBiso mean: 40.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.53 Å20 Å20 Å2
2---3.53 Å20 Å2
3---7.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4182 0 0 84 4266
Refine LS restraints
Refine-IDTypeDev ideal
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_d23.1
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_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.387 409 3.4 %
Rwork0.337 11791 -
obs--79.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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