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- PDB-4bc4: Crystal structure of human D-xylulokinase in complex with D-xylulose -

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Basic information

Entry
Database: PDB / ID: 4bc4
TitleCrystal structure of human D-xylulokinase in complex with D-xylulose
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
D-XYLULOSE / Xylulose kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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 1.2Dec 19, 2012Group: Atomic model / Database references / Other
Revision 1.3Jan 30, 2013Group: Database references
Revision 1.4Jun 3, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_sheet_hbond ...pdbx_database_status / pdbx_struct_sheet_hbond / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _pdbx_database_status.status_code_sf / _struct_conf.pdbx_PDB_helix_id ..._pdbx_database_status.status_code_sf / _struct_conf.pdbx_PDB_helix_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id

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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)178,1649
Polymers177,5273
Non-polymers6376
Water13,313739
1
A: XYLULOSE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3883
Polymers59,1761
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: XYLULOSE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3883
Polymers59,1761
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: XYLULOSE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3883
Polymers59,1761
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.800, 102.800, 159.350
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: Sugar ChemComp-XUL / D-XYLULOSE / Xylulose


Type: D-saccharide / Mass: 150.130 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 739 / 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, 15% 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: 1.79→59.37 Å / Num. obs: 177198 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Biso Wilson estimate: 30.02 Å2 / Rmerge(I) obs: 0.22 / Net I/σ(I): 9.7
Reflection shellResolution: 1.79→1.82 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 0.5 / % possible all: 99.6

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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: 1.79→59.37 Å / Cor.coef. Fo:Fc: 0.9614 / Cor.coef. Fo:Fc free: 0.9556 / SU R Cruickshank DPI: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.093 / SU Rfree Blow DPI: 0.088 / SU Rfree Cruickshank DPI: 0.091
RfactorNum. reflection% reflectionSelection details
Rfree0.1865 8724 5.03 %RANDOM
Rwork0.167 ---
obs0.1679 173284 97.63 %-
Displacement parametersBiso mean: 35.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.8064 Å20 Å20 Å2
2---0.8064 Å20 Å2
3---1.6128 Å2
Refine analyzeLuzzati coordinate error obs: 0.209 Å
Refinement stepCycle: LAST / Resolution: 1.79→59.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11944 0 42 739 12725
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0123772HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0642756HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6509SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes283HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3656HARMONIC5
X-RAY DIFFRACTIONt_it23772HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.35
X-RAY DIFFRACTIONt_other_torsion2.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1583SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact25975SEMIHARMONIC4
LS refinement shellResolution: 1.79→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2655 516 5.11 %
Rwork0.2504 9583 -
all0.2512 10099 -
obs--97.63 %
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)
10.6093-0.01510.12270.6229-0.011.1672-0.0076-0.00920.029-0.0089-0.00830.0745-0.0541-0.00010.0159-0.0515-0.06410.0223-0.054-0.0282-0.1093-57.4009-21.49388.7395
20.94330.1005-0.25660.53240.01390.97580.05160.085-0.00410.0544-0.0025-0.04560.1076-0.0625-0.0491-0.0111-0.0141-0.0421-0.09270.0163-0.0991-40.447228.3361-1.3082
30.87430.3020.18770.76030.10090.9799-0.06370.0335-0.2107-0.03830.0454-0.161-0.0540.00520.0183-0.10950.02910.0242-0.0213-0.0163-0.0904-8.1461-9.16874.005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1A
2X-RAY DIFFRACTION2B
3X-RAY DIFFRACTION3C

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