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- PDB-4bc3: Crystal structure of human D-xylulokinase -

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Basic information

Entry
Database: PDB / ID: 4bc3
TitleCrystal structure of human D-xylulokinase
ComponentsXYLULOSE KINASE
KeywordsTRANSFERASE / GLUCURONATE XYLULOKINASE PATHWAY
Function / homology
Function and homology information


xylulose metabolic process / D-xylulokinase activity / xylulokinase / xylulose catabolic process / glucuronate catabolic process to xylulose 5-phosphate / Formation of xylulose-5-phosphate / D-xylose metabolic process / generation of precursor metabolites and energy / carbohydrate metabolic process / phosphorylation ...xylulose metabolic process / D-xylulokinase activity / xylulokinase / xylulose catabolic process / glucuronate catabolic process to xylulose 5-phosphate / Formation of xylulose-5-phosphate / D-xylose metabolic process / generation of precursor metabolites and energy / carbohydrate metabolic process / phosphorylation / ATP binding / cytosol
Similarity search - Function
D-xylulose kinase / 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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsBunker, R.D. / Loomes, K.M. / Baker, E.N.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structure and Function of Human Xylulokinase, an Enzyme with Important Roles in Carbohydrate Metabolism
Authors: Bunker, R.D. / Bulloch, E.M.M. / Dickson, J.M.J. / Loomes, K.M. / Baker, E.N.
History
DepositionOct 1, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Jan 30, 2013Group: Database references
Revision 1.3Feb 13, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: XYLULOSE KINASE
B: XYLULOSE KINASE
C: XYLULOSE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,14813
Polymers177,5273
Non-polymers62110
Water21,3841187
1
A: XYLULOSE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4866
Polymers59,1761
Non-polymers3105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: XYLULOSE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3003
Polymers59,1761
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: XYLULOSE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3624
Polymers59,1761
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.790, 99.790, 157.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein XYLULOSE KINASE / XYLULOKINASE / D-XYLULOKINASE


Mass: 59175.680 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPROEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O75191, xylulokinase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1187 / 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: 2.8 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growDetails: 200 MM MES/KOH, PH 5.9, 13% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 0.8856
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 13, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.68→58.25 Å / Num. obs: 200085 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 27.01 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 9.4
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 8 % / Mean I/σ(I) obs: 0.6 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN D-XYLULOSE DETERMINED BY TWO-ENERGY SELENIUM MAD

Resolution: 1.68→58.22 Å / Cor.coef. Fo:Fc: 0.9656 / Cor.coef. Fo:Fc free: 0.9564 / SU R Cruickshank DPI: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.079 / SU Rfree Blow DPI: 0.078 / SU Rfree Cruickshank DPI: 0.08
RfactorNum. reflection% reflectionSelection details
Rfree0.1836 9906 5.02 %RANDOM
Rwork0.1586 ---
obs0.1598 197305 98.64 %-
Displacement parametersBiso mean: 31.02 Å2
Baniso -1Baniso -2Baniso -3
1--1.2531 Å20 Å20 Å2
2---1.2531 Å20 Å2
3---2.5063 Å2
Refine analyzeLuzzati coordinate error obs: 0.204 Å
Refinement stepCycle: LAST / Resolution: 1.68→58.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11972 0 40 1187 13199
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0123797HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0442777HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6511SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes283HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3650HARMONIC5
X-RAY DIFFRACTIONt_it23797HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.5
X-RAY DIFFRACTIONt_other_torsion2.77
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1581SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact27306SEMIHARMONIC4
LS refinement shellResolution: 1.68→1.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2837 665 5.12 %
Rwork0.25 12332 -
all0.2518 12997 -
obs--98.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.62760.0387-0.11990.9316-0.16240.8530.0802-0.10170.03340.0072-0.11840.1392-0.01070.07810.0382-0.1135-0.0296-0.0061-0.0099-0.0436-0.0863-4.273311.516625.3195
20.88380.0282-0.50140.34550.12140.64410.02520.00980.11590.0647-0.01190.00170.0608-0.0138-0.01330.00690.0025-0.009-0.04880.0277-0.07939.910858.678930.6767
30.63670.13090.30090.84250.35580.88230.0271-0.0985-0.0893-0.0745-0.0571-0.0533-0.0911-0.12310.03-0.12120.03240.02490.02480.0296-0.084543.743621.12119.9142
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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