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- PDB-3i8b: The crystal structure of xylulose kinase from Bifidobacterium ado... -

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Basic information

Entry
Database: PDB / ID: 3i8b
TitleThe crystal structure of xylulose kinase from Bifidobacterium adolescentis
ComponentsXylulose kinase
KeywordsTRANSFERASE / Xylulose kinase / Bifidobacterium adolescentis / strain ATCC 15703 / DSM 20083 / 11200j / Kinase / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


xylulokinase / phosphotransferase activity, alcohol group as acceptor / kinase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Xylulokinase / FGGY family of carbohydrate kinases signature 1. / 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 ...Xylulokinase / FGGY family of carbohydrate kinases signature 1. / 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
Biological speciesBifidobacterium adolescentis ATCC 15703 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsZhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of xylulose kinase from Bifidobacterium adolescentis
Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S.
History
DepositionJul 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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_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_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

Downloads & links

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Assembly

Deposited unit
A: Xylulose kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2572
Polymers54,2331
Non-polymers241
Water6,630368
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Xylulose kinase
hetero molecules

A: Xylulose kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,5154
Polymers108,4662
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2090 Å2
ΔGint-31 kcal/mol
Surface area37350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.732, 61.918, 94.606
Angle α, β, γ (deg.)90.00, 93.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Xylulose kinase


Mass: 54233.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium adolescentis ATCC 15703 (bacteria)
Strain: ATCC 15703 / DSM 20083 / Gene: xylB / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Codon+RIL-stratagene / References: UniProt: A1A0I0
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M Ammonium acetate, 0.1 M sodium acetate trihydrate pH 4.6, 30% w/v PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 24, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2→52.13 Å / Num. all: 37936 / Num. obs: 37936 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 10.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 3.6 / Num. unique all: 5506 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→48.298 Å / SU ML: 0.26 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.22 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1912 5.04 %RANDOM
Rwork0.1805 ---
obs0.1828 37928 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.702 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso mean: 13.87 Å2
Baniso -1Baniso -2Baniso -3
1--9.173 Å20 Å2-2.186 Å2
2---4.1887 Å2-0 Å2
3---8.1409 Å2
Refinement stepCycle: LAST / Resolution: 2→48.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3714 0 1 368 4083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083786
X-RAY DIFFRACTIONf_angle_d1.0945166
X-RAY DIFFRACTIONf_dihedral_angle_d17.4571333
X-RAY DIFFRACTIONf_chiral_restr0.076590
X-RAY DIFFRACTIONf_plane_restr0.005687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.26931360.22752590X-RAY DIFFRACTION100
2.05-2.10550.25261410.21632505X-RAY DIFFRACTION100
2.1055-2.16740.25841270.19712556X-RAY DIFFRACTION100
2.1674-2.23740.24151220.19182560X-RAY DIFFRACTION100
2.2374-2.31730.24491370.18312585X-RAY DIFFRACTION100
2.3173-2.41010.21291440.17832538X-RAY DIFFRACTION100
2.4101-2.51980.25041370.18692562X-RAY DIFFRACTION100
2.5198-2.65260.23831290.19652551X-RAY DIFFRACTION100
2.6526-2.81880.23921360.1852595X-RAY DIFFRACTION100
2.8188-3.03640.24021350.18072576X-RAY DIFFRACTION100
3.0364-3.34190.21761400.1822562X-RAY DIFFRACTION100
3.3419-3.82530.21041470.15952587X-RAY DIFFRACTION100
3.8253-4.81880.17561470.14442582X-RAY DIFFRACTION100
4.8188-48.31180.20221340.16342667X-RAY DIFFRACTION100

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