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- PDB-1cza: MUTANT MONOMER OF RECOMBINANT HUMAN HEXOKINASE TYPE I COMPLEXED W... -

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Entry
Database: PDB / ID: 1cza
TitleMUTANT MONOMER OF RECOMBINANT HUMAN HEXOKINASE TYPE I COMPLEXED WITH GLUCOSE, GLUCOSE-6-PHOSPHATE, AND ADP
ComponentsHEXOKINASE TYPE I
KeywordsTRANSFERASE / STRUCTURALLY HOMOLOGOUS DOMAINS
Function / homologyGlycolysis / Defective HK1 causes hexokinase deficiency (HK deficiency) / Hexokinase domain profile. / Hexokinase domain signature. / Hexokinase / Hexokinase / Hexokinase, C-terminal / Hexokinase, N-terminal / Hexokinase, binding site / Hexokinase ...Glycolysis / Defective HK1 causes hexokinase deficiency (HK deficiency) / Hexokinase domain profile. / Hexokinase domain signature. / Hexokinase / Hexokinase / Hexokinase, C-terminal / Hexokinase, N-terminal / Hexokinase, binding site / Hexokinase / hexokinase / hexokinase activity / establishment of protein localization to mitochondrion / maintenance of protein location in mitochondrion / carbohydrate phosphorylation / mannokinase activity / fructokinase activity / glucokinase activity / peptidoglycan binding / glucose binding / canonical glycolysis / positive regulation of interleukin-1 beta secretion / cellular glucose homeostasis / positive regulation of cytokine secretion involved in immune response / glycolytic process / mitochondrial outer membrane / membrane raft / mitochondrion / ATP binding / identical protein binding / cytosol / Hexokinase-1
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 1.9 Å resolution
AuthorsAleshin, A.E. / Liu, X. / Kirby, C. / Bourenkov, G.P. / Bartunik, H.D. / Fromm, H.J. / Honzatko, R.B.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystal structures of mutant monomeric hexokinase I reveal multiple ADP binding sites and conformational changes relevant to allosteric regulation.
Authors: Aleshin, A.E. / Kirby, C. / Liu, X. / Bourenkov, G.P. / Bartunik, H.D. / Fromm, H.J. / Honzatko, R.B.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Regulation of Hexokinase I: Crystal Structure of Recombinant Human Brain Hexokinase Complexed with Glucose and Phosphate
Authors: Aleshin, A.E. / Zeng, C. / Bartunik, H.D. / Fromm, H.J. / Honzatko, R.B.
#2: Journal: Structure / Year: 1998
Title: The Mechanism of Regulation of Hexokinase: New Insights from the Crystal Structure of Recombinant Human Brain Hexokinase Complexed with Glucose and Glucose-6-Phosphate
Authors: Aleshin, A.E. / Zeng, C. / Bourenkov, G.P. / Bartunik, H.D. / Fromm, H.J. / Honzatko, R.B.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 1, 1999 / Release: Mar 6, 2000
RevisionDateData content typeGroupProviderType
1.0Mar 6, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
N: HEXOKINASE TYPE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,8956
Polyers102,5871
Non-polymers1,3085
Water12,106672
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)145.660, 145.800, 58.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP 21 21 2

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Components

#1: Protein/peptide HEXOKINASE TYPE I


Mass: 102587.008 Da / Num. of mol.: 1 / Mutation: E280A, R283A, G284Y / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Cell: NEURON / Organ: BRAIN / Plasmid name: PET11A / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P19367, hexokinase
#2: Chemical ChemComp-GLC / ALPHA-D-GLUCOSE


Mass: 180.156 Da / Num. of mol.: 2 / Formula: C6H12O6 / Glucose
#3: Chemical ChemComp-G6P / ALPHA-D-GLUCOSE-6-PHOSPHATE


Mass: 260.136 Da / Num. of mol.: 2 / Formula: C6H13O9P
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / Formula: H2O / Water
Compound detailsWILD-TYPE HEXOKINASE I IS A MONOMER AT CONCENTRATION BELOW 1 MG/ML. THE MUTANT IN THIS ENTRY IS A ...WILD-TYPE HEXOKINASE I IS A MONOMER AT CONCENTRATION BELOW 1 MG/ML. THE MUTANT IN THIS ENTRY IS A MONOMER AT CONCENTRATION UP TO 15 MG/ML.

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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: 3.01 / Density percent sol: 59.11 %
Crystal growTemp: 298 K / Method: evaporation / pH: 6.5
Details: PEG 8000, SODIUM ACETATE, MES, ADP, ALUMINUM NITRATE, SODIUM FLUORIDE, MAGNESIUM ACETATE, GLUCOSE, pH 6.5, EVAPORATION, temperature 298.0K
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
120 mg/mlprotein11
214-18 %PEG800012
3100 mMMES12
4150-250 mMsodium acetate12
520 mMADP12

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Data collection

DiffractionMean temperature: 110 kelvins
SourceSource: SYNCHROTRON / Type: EMBL/DESY, HAMBURG BEAMLINE BW7B / Synchrotron site: EMBL/DESY, Hamburg / Beamline: BW7B / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: CCD / Collection date: Sep 6, 1998
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 30.6 Å2 / D resolution high: 1.9 Å / D resolution low: 17 Å / Number all: 96631 / Number obs: 96631 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.055 / NetI over sigmaI: 16.8 / Redundancy: 4.7 % / Percent possible obs: 98.3
Reflection shellRmerge I obs: 0.55 / Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / Redundancy: 4 % / Percent possible all: 98.3
Reflection
*PLUS
Number obs: 83349 / Number measured all: 286697 / Percent possible obs: 98.6 / Rmerge I obs: 0.048
Reflection shell
*PLUS
Percent possible obs: 82.3 / Rmerge I obs: 0.41

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefineDetails: USED MAXIMUM LIKELIHOOD RESIDUALS AND CONJUGATE DIRECTION MINIMIZATION ADP is bound near the N-terminus of the polypeptide chain. Side chains of residues 16, 20, 24, 101, 102, 353, 794, 801, 811 have poor electron density. Their occupancies are set to 0.01.
R Free selection details: RANDOM / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: ENGH & HUBER
Least-squares processR factor R free: 0.258 / R factor R work: 0.211 / R factor all: 0.213 / R factor obs: 0.213 / Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Number reflection R free: 4769 / Number reflection all: 95270 / Number reflection obs: 95270 / Percent reflection obs: 100
Refine hist #LASTHighest resolution: 1.9 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 7097 / Nucleic acid: 0 / Ligand: 83 / Solvent: 679 / Total: 7859
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d0.033
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Least-squares process
*PLUS
R factor R free: 0.268 / Highest resolution: 2 Å
Refine LS restraints
*PLUS
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0360.04

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