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- PDB-4bc2: Crystal structure of human D-xylulokinase in complex with D-xylul... -

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Basic information

Entry
Database: PDB / ID: 4bc2
TitleCrystal structure of human D-xylulokinase in complex with D-xylulose and adenosine diphosphate
ComponentsXYLULOSE KINASE
KeywordsTRANSFERASE / GLUCURONATE XYLULOKINASE PATHWAY / FGGY CARBOHYDRATE KINASE
Function / homology
Function and homology information


xylulokinase / xylulose catabolic process / Formation of xylulose-5-phosphate / D-glucuronate catabolic process to D-xylulose 5-phosphate / xylulose metabolic process / D-xylulokinase activity / D-xylose metabolic process / generation of precursor metabolites and energy / carbohydrate metabolic process / 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
ADENOSINE-5'-DIPHOSPHATE / D-XYLULOSE / Xylulose kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 1.4Feb 6, 2013Group: Atomic model
Revision 1.5Jul 8, 2020Group: Derived calculations / Other / Category: pdbx_database_status / struct_conn
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)179,32110
Polymers177,5273
Non-polymers1,7947
Water13,187732
1
A: XYLULOSE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7533
Polymers59,1761
Non-polymers5772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: XYLULOSE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8154
Polymers59,1761
Non-polymers6393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: XYLULOSE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7533
Polymers59,1761
Non-polymers5772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.160, 102.160, 159.390
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 / D-XYLULOKINASE / 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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Sugar ChemComp-XUL / D-XYLULOSE


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 732 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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% (W/V) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.97→36.8 Å / Num. obs: 131532 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 37.64 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.8
Reflection shellResolution: 1.97→2 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 0.5 / % possible all: 99.8

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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: 1.97→36.82 Å / Cor.coef. Fo:Fc: 0.9546 / Cor.coef. Fo:Fc free: 0.9448 / SU R Cruickshank DPI: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.133 / SU Rfree Blow DPI: 0.119 / SU Rfree Cruickshank DPI: 0.123
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.1972 6465 5.01 %RANDOM
Rwork0.1732 ---
obs0.1744 128989 98.1 %-
Displacement parametersBiso mean: 45.83 Å2
Baniso -1Baniso -2Baniso -3
1--2.7559 Å20 Å20 Å2
2---2.7559 Å20 Å2
3---5.5118 Å2
Refine analyzeLuzzati coordinate error obs: 0.264 Å
Refinement stepCycle: LAST / Resolution: 1.97→36.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11988 0 95 732 12815
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0124078HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0543346HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6574SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes284HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3735HARMONIC5
X-RAY DIFFRACTIONt_it24078HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.15
X-RAY DIFFRACTIONt_other_torsion2.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1607SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies7HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact26871SEMIHARMONIC4
LS refinement shellResolution: 1.97→2.02 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2581 391 5.13 %
Rwork0.2484 7238 -
all0.2489 7629 -
obs--98.1 %
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)
10.6162-0.08140.24680.7593-0.43991.2120.0466-0.07960.0385-0.0177-0.05890.08150.0361-0.02470.0123-0.1414-0.01240.00780.0776-0.0517-0.0956-4.14119.7576-3.5067
20.51810.0132-0.02520.74230.07751.5927-0.0545-0.0327-0.06-0.00950.0453-0.0230.02910.10440.0092-0.18640.05690.02590.07670.052-0.104247.004820.29016.7385
31.5785-0.0805-0.59330.79460.41171.43880.25240.2120.39590.0185-0.138-0.1487-0.1523-0.1923-0.1144-0.03890.10910.0642-0.11210.0761-0.115911.923356.43251.8399
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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