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- PDB-3hz6: Crystal structure of xylulokinase from Chromobacterium violaceum -

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Basic information

Entry
Database: PDB / ID: 3hz6
TitleCrystal structure of xylulokinase from Chromobacterium violaceum
ComponentsXylulokinase
KeywordsTRANSFERASE / xylulose / xylulokinase / 11200b1 / structural genomic / Chromobacterium violaceum / manolate / Kinase / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


D-xylulokinase activity / xylulokinase / nucleotide binding
Similarity search - Function
FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 ...FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / Carbohydrate kinase, FGGY / Carbohydrate kinase, FGGY, N-terminal / FGGY family of carbohydrate kinases, N-terminal domain / Carbohydrate kinase, FGGY, C-terminal / FGGY family of carbohydrate kinases, C-terminal domain / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / MALONATE ION / PHOSPHATE ION / D-XYLULOSE / Xylulokinase
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsZhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of xylulokinase from Chromobacterium violaceum
Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S.
History
DepositionJun 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xylulokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0377
Polymers56,0781
Non-polymers9596
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.512, 159.427, 47.185
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-967-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Xylulokinase


Mass: 56078.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Gene: CV_1862, xylB / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Coden+RIL-stratagene / References: UniProt: Q7NWW7, xylulokinase
#6: Sugar ChemComp-XUL / D-XYLULOSE


Type: D-saccharide / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5

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Non-polymers , 5 types, 529 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium manolate pH 7.0, 20% w/v Polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→79.71 Å / Num. obs: 64992 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Biso Wilson estimate: 15.29 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 22.4
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 6.1 / Num. unique all: 8676 / % possible all: 91.4

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.65→47.185 Å / SU ML: 0.2 / Isotropic thermal model: Isotropic / σ(F): 1.82 / σ(I): 0 / Phase error: 16.28 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1927 3300 5.08 %Random
Rwork0.1625 ---
obs0.1641 64930 98.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.227 Å2 / ksol: 0.387 e/Å3
Displacement parametersBiso mean: 15.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.0349 Å2-0 Å20 Å2
2---1.9856 Å2-0 Å2
3---1.9507 Å2
Refinement stepCycle: LAST / Resolution: 1.65→47.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 61 524 4381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.67360.18081280.14972134X-RAY DIFFRACTION84
1.6736-1.69860.18061380.14962305X-RAY DIFFRACTION90
1.6986-1.72510.19431300.13962442X-RAY DIFFRACTION96
1.7251-1.75340.171450.13842566X-RAY DIFFRACTION99
1.7534-1.78360.18251110.13912591X-RAY DIFFRACTION100
1.7836-1.81610.17041490.152573X-RAY DIFFRACTION100
1.8161-1.8510.19731250.14212552X-RAY DIFFRACTION100
1.851-1.88880.1791480.14742607X-RAY DIFFRACTION100
1.8888-1.92980.18691440.14072532X-RAY DIFFRACTION100
1.9298-1.97470.1821280.14792595X-RAY DIFFRACTION100
1.9747-2.02410.19521480.14282564X-RAY DIFFRACTION100
2.0241-2.07880.19441570.14292569X-RAY DIFFRACTION100
2.0788-2.140.16171330.14332607X-RAY DIFFRACTION100
2.14-2.20910.20621410.14572578X-RAY DIFFRACTION100
2.2091-2.2880.19971410.15422593X-RAY DIFFRACTION100
2.288-2.37970.18721290.15932628X-RAY DIFFRACTION100
2.3797-2.48790.18561250.15952604X-RAY DIFFRACTION100
2.4879-2.61910.21261350.16652622X-RAY DIFFRACTION100
2.6191-2.78320.20081330.17692624X-RAY DIFFRACTION100
2.7832-2.9980.21211490.17122609X-RAY DIFFRACTION100
2.998-3.29970.21541430.17092652X-RAY DIFFRACTION100
3.2997-3.7770.18091380.15282658X-RAY DIFFRACTION100
3.777-4.75790.16021320.1512711X-RAY DIFFRACTION100
4.7579-47.20430.19371500.20042714X-RAY DIFFRACTION96

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