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- PDB-2qm1: Crystal structure of glucokinase from Enterococcus faecalis -

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Basic information

Entry
Database: PDB / ID: 2qm1
TitleCrystal structure of glucokinase from Enterococcus faecalis
ComponentsGlucokinase
KeywordsTRANSFERASE / alpha-beta structure / putative helix-turn-helix / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


glucokinase / glucokinase activity / glycolytic process / metal ion binding / cytoplasm
Similarity search - Function
Glucokinase ROK / 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
DI(HYDROXYETHYL)ETHER / Glucokinase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.02 Å
AuthorsKim, Y. / Joachimiak, G. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Glucokinase from Enterococcus faecalis.
Authors: Kim, Y. / Joachimiak, G. / Moy, S. / Joachimiak, A.
History
DepositionJul 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Remark 300 BIOMOLECULE: 1, 2 AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. SEE REMARK ... BIOMOLECULE: 1, 2 AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)140,14422
Polymers138,9104
Non-polymers1,23418
Water16,484915
1
A: Glucokinase
B: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,00310
Polymers69,4552
Non-polymers5488
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400/27150
MethodPISA
2
C: Glucokinase
D: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,14112
Polymers69,4552
Non-polymers68610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890/27140
MethodPISA
Unit cell
Length a, b, c (Å)62.083, 131.260, 82.763
Angle α, β, γ (deg.)90.00, 92.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glucokinase


Mass: 34727.582 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: glcK, EF_2788 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q830J4

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Non-polymers , 6 types, 933 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 915 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 0.2M NaCl, 0.1M Bis-Tris pH 5.7, 22.5% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2005 / Details: mirrors
RadiationMonochromator: double crystal, Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. all: 86418 / Num. obs: 86418 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rsym value: 0.112 / Net I/σ(I): 7.9
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.32 / Num. unique all: 8197 / Rsym value: 0.241 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data collection
HKL-2000data reduction
HKL-2000data scaling
autoSHARPphasing
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.02→39.43 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.112 / SU ML: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.182
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.23 8647 10 %RANDOM
Rwork0.186 ---
all0.19 77409 --
obs0.19 77409 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.643 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å2-1.07 Å2
2---2.19 Å20 Å2
3---1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.02→39.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9641 0 62 915 10618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02210368
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.95514101
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45151407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.20525.528445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.518151738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7031543
X-RAY DIFFRACTIONr_chiral_restr0.1290.21594
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027957
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.25592
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.27305
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2878
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1690.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.299
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0291.56886
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.558210791
X-RAY DIFFRACTIONr_scbond_it2.88533894
X-RAY DIFFRACTIONr_scangle_it4.3364.53310
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.02→2.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 627 -
Rwork0.218 5403 -
obs-6021 94.06 %
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)
10.475-0.2006-0.06751.1628-0.04090.5999-0.015-0.031-0.07820.02450.01430.08710.0651-0.06360.0007-0.2372-0.0278-0.0053-0.22360.0049-0.252632.392253.198838.0017
20.3970.0925-0.04770.4889-0.02040.52460.0077-0.01330.06980.01060.00690.0195-0.06730.0127-0.0146-0.21570.0069-0.0019-0.228-0.0018-0.232844.85784.722541.6986
30.42670.1282-0.00231.2188-0.10240.6807-0.03760.03790.05020.01650.06830.1981-0.0557-0.0665-0.0307-0.23630.02620.0234-0.20990.027-0.23442.5852116.02373.1244
40.3008-0.21530.14370.5677-0.28080.68920.04770.0531-0.0264-0.0751-0.0150.02510.10290.0209-0.0327-0.2082-0.00070.0115-0.22190.0021-0.242816.801884.7326-0.2884
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3214 - 324
2X-RAY DIFFRACTION2BB1 - 3224 - 325
3X-RAY DIFFRACTION3CC1 - 3214 - 324
4X-RAY DIFFRACTION4DD1 - 3214 - 324

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