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- PDB-3vov: Crystal Structure of ROK Hexokinase from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 3vov
TitleCrystal Structure of ROK Hexokinase from Thermus thermophilus
ComponentsGlucokinase
KeywordsTRANSFERASE / ROK / hexokinase / glucokinase / sugar kinase
Function / homology
Function and homology information


kinase activity / metal ion binding
Similarity search - Function
ROK family signature. / ROK family / ROK family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsNakamura, T. / Kashima, Y. / Mine, S. / Oku, T. / Uegaki, K.
CitationJournal: J.Biosci.Bioeng. / Year: 2012
Title: Characterization and crystal structure of the thermophilic ROK hexokinase from Thermus thermophilus
Authors: Nakamura, T. / Kashima, Y. / Mine, S. / Oku, T. / Uegaki, K.
History
DepositionFeb 21, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucokinase
B: Glucokinase
C: Glucokinase
D: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,78613
Polymers126,0644
Non-polymers7229
Water8,035446
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13870 Å2
ΔGint-60 kcal/mol
Surface area42490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.926, 138.144, 75.156
Angle α, β, γ (deg.)90.00, 95.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glucokinase / hexokinase


Mass: 31515.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA0299 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SLJ4, hexokinase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl (pH 8.5), 8% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. all: 93722 / Num. obs: 93458 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.6
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 3.22 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→33.6 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.457 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22537 4686 5 %RANDOM
Rwork0.18091 ---
obs0.18308 88643 99.6 %-
all-93458 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.885 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.02→33.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8694 0 34 446 9174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0228916
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.99612053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.22551184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.53722.216379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.579151419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.04615107
X-RAY DIFFRACTIONr_chiral_restr0.1210.21327
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026857
X-RAY DIFFRACTIONr_nbd_refined0.2120.24546
X-RAY DIFFRACTIONr_nbtor_refined0.3070.26045
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2566
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.29
X-RAY DIFFRACTIONr_mcbond_it1.5371.55957
X-RAY DIFFRACTIONr_mcangle_it1.79529074
X-RAY DIFFRACTIONr_scbond_it2.74833315
X-RAY DIFFRACTIONr_scangle_it4.4084.52973
LS refinement shellResolution: 2.023→2.075 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 312 -
Rwork0.209 6495 -
obs--98.9 %

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