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- PDB-4f9o: Crystal Structure of recombinant human Hexokinase type I with 2-d... -

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Basic information

Entry
Database: PDB / ID: 4f9o
TitleCrystal Structure of recombinant human Hexokinase type I with 2-deoxy-Glucose 6-Phosphate
ComponentsHexokinase-1
KeywordsTRANSFERASE / hexokinase / 2-deoxy Glucose-6-Phosphate
Function / homology
Function and homology information


Defective HK1 causes hexokinase deficiency (HK deficiency) / glucosamine kinase activity / Synthesis of GDP-mannose / hexokinase activity / maintenance of protein location in mitochondrion / mannokinase activity / establishment of protein localization to mitochondrion / hexokinase / positive regulation of cytokine production involved in immune response / fructokinase activity ...Defective HK1 causes hexokinase deficiency (HK deficiency) / glucosamine kinase activity / Synthesis of GDP-mannose / hexokinase activity / maintenance of protein location in mitochondrion / mannokinase activity / establishment of protein localization to mitochondrion / hexokinase / positive regulation of cytokine production involved in immune response / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / mannose metabolic process / glucose 6-phosphate metabolic process / peptidoglycan binding / D-glucose binding / fructose 6-phosphate metabolic process / canonical glycolysis / Glycolysis / intracellular glucose homeostasis / positive regulation of interleukin-1 beta production / glycolytic process / glucose metabolic process / mitochondrial outer membrane / inflammatory response / membrane raft / innate immune response / mitochondrion / ATP binding / cytosol
Similarity search - Function
Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. ...Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-deoxy-6-O-phosphono-beta-D-glucopyranose / beta-D-glucopyranose / CITRIC ACID / Hexokinase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsShen, L. / Honzatko, R.B.
CitationJournal: to be published
Title: Inhibitor Sites of Unequal Affinity Linked by Binding Synergism in Mutant Forms of Recombinant Human Hexokinase Type-I
Authors: Shen, L. / Gao, Y. / Honzatko, R.B.
History
DepositionMay 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hexokinase-1
B: Hexokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,74115
Polymers204,7602
Non-polymers1,98113
Water5,477304
1
A: Hexokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2747
Polymers102,3801
Non-polymers8956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hexokinase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4668
Polymers102,3801
Non-polymers1,0877
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.980, 122.090, 120.350
Angle α, β, γ (deg.)90.000, 92.970, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 1007
2114B1 - 1007

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hexokinase-1 / Brain form hexokinase / Hexokinase type I / HK I


Mass: 102379.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HK1 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19367, hexokinase

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Sugars , 2 types, 8 molecules

#2: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar
ChemComp-0NZ / 2-deoxy-6-O-phosphono-beta-D-glucopyranose / 2-deoxy-6-O-phosphono-beta-D-arabino-hexopyranose / 2-deoxy-beta-D-glucopyranose 6-phosphate / 2-deoxy-6-O-phosphono-beta-D-glucose / 2-deoxy-6-O-phosphono-D-glucose / 2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 244.136 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13O8P
IdentifierTypeProgram
b-D-2-deoxy-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 309 molecules

#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 277 K / Method: hanging drop / pH: 6
Details: PEG 4000, PEG 8000, sodium acetate, sodium citrate, pH 6.0, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2
DetectorType: NOIR-1 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.65→35.36 Å / Num. obs: 69139 / % possible obs: 99.3 % / Redundancy: 3.82 % / Rmerge(I) obs: 0.086 / Χ2: 0.95 / Net I/σ(I): 8.4 / Scaling rejects: 2000
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.65-2.743.710.2933.32576868621.299
2.74-2.853.850.2114.42661968891.0599.1
2.85-2.983.870.1765.1266966872199.2
2.98-3.143.880.1376.12680868800.9399.4
3.14-3.343.880.1197.22690269070.9499.4
3.34-3.63.80.1296.62668469051.0399.5
3.6-3.963.730.1118.22629269150.9299.4
3.96-4.533.870.06513.52696869340.8399.7
4.53-5.73.860.06912.72705569890.7699.6
5.7-35.363.790.05416.22662769860.8798.8

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Processing

Software
NameVersionClassificationNB
d*TREK9.7Ldata reduction
REFMAC5.5.0066refinement
PDB_EXTRACT3.11data extraction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→35.36 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.561 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.911 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2578 3466 5 %RANDOM
Rwork0.2397 ---
all0.293 69139 --
obs0.2406 68856 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 123.61 Å2 / Biso mean: 55.3717 Å2 / Biso min: 16.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20.12 Å2
2--0.04 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.65→35.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14066 0 125 304 14495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02214410
X-RAY DIFFRACTIONr_angle_refined_deg0.8651.98119406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.46651796
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.74123.846650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.207152676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.14315118
X-RAY DIFFRACTIONr_chiral_restr0.0560.22222
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210614
X-RAY DIFFRACTIONr_mcbond_it0.8131.58876
X-RAY DIFFRACTIONr_mcangle_it1.54214310
X-RAY DIFFRACTIONr_scbond_it1.40235534
X-RAY DIFFRACTIONr_scangle_it2.5374.55096
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 7102 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.410.5
MEDIUM THERMAL1.172
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 252 -
Rwork0.348 4784 -
all-5036 -
obs--98.32 %

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