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- PDB-3d7e: Enterococcus casseliflavus glycerol kinase mutant HIS232ALA compl... -

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Basic information

Entry
Database: PDB / ID: 3d7e
TitleEnterococcus casseliflavus glycerol kinase mutant HIS232ALA complexed with glycerol
ComponentsGlycerol kinase
KeywordsTRANSFERASE / KINASE / ATP-binding / Glycerol metabolism / Nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


glycerol-3-phosphate metabolic process / glycerol kinase / glycerol kinase activity / glycerol metabolic process / glycerol catabolic process / ATP binding / cytosol
Similarity search - Function
FGGY family of carbohydrate kinases signature 1. / Glycerol kinase / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / 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 ...FGGY family of carbohydrate kinases signature 1. / Glycerol kinase / FGGY family of carbohydrate kinases signature 2. / Carbohydrate kinase, FGGY, conserved site / 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
Biological speciesEnterococcus casseliflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsYeh, J.I. / Vahedi-Faridi, A.
Citation
Journal: Biochemistry / Year: 2009
Title: Structural characterizations of glycerol kinase: unraveling phosphorylation-induced long-range activation
Authors: Yeh, J.I. / Kettering, R. / Saxl, R. / Bourand, A. / Darbon, E. / Joly, N. / Briozzo, P. / Deutscher, J.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2005
Title: The effects of flash-annealing on glycerol kinase crystals
Authors: Vahedi-Faridi, A. / Stojanoff, V. / Yeh, J.I.
History
DepositionMay 21, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 28, 2012Group: Structure summary
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 1, 2023Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
O: Glycerol kinase
X: Glycerol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4134
Polymers111,2282
Non-polymers1842
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-16 kcal/mol
Surface area34160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.572, 200.019, 56.431
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Glycerol kinase / ATP:glycerol 3-phosphotransferase / Glycerokinase / GK


Mass: 55614.223 Da / Num. of mol.: 2 / Mutation: H232A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus casseliflavus (bacteria) / Gene: glpK / Plasmid: POXO4 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: O34153, glycerol kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 49.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 29% PEG400, 0.1M sodium acetate, 0.1M calcium acetate, 10% glycerol, PH4.50, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.033
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 63332 / % possible obs: 89 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.8
Reflection shellResolution: 2.03→2.1 Å / Rmerge(I) obs: 0.261

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Processing

Software
NameVersionClassification
XFITdata reduction
REFMAC5.2.0019refinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XUP

1xup


Resolution: 2.03→39.28 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.906 / SU B: 2.572 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3224 5.1 %RANDOM
Rwork0.19075 ---
obs0.19075 63284 88.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.812 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.03→39.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7676 0 12 307 7995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0380.0227858
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5941.94110654
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5765988
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69225.355366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.266151314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9271530
X-RAY DIFFRACTIONr_chiral_restr0.2130.21168
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.025988
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2420.24068
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.25447
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2484
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.2104
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9791.55142
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.63927834
X-RAY DIFFRACTIONr_scbond_it4.31333344
X-RAY DIFFRACTIONr_scangle_it5.964.52820
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.027→2.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 141 -
Rwork0.173 2713 -
obs--52.22 %
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)
10.6211-0.3632-0.04150.90870.04910.12980.03310.02070.07730.054-0.0606-0.02760.0251-0.00510.0275-0.0301-0.01940.0059-0.03020.0095-0.065673.996223.5092-11.5139
20.5382-0.2654-0.00480.7093-0.17160.1655-0.0068-0.0329-0.07140.0403-0.0180.004-0.01970.010.0247-0.02160.0016-0.0137-0.02970.01-0.055869.107-27.773-18.859
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1O5 - 227
2X-RAY DIFFRACTION1O240 - 260
3X-RAY DIFFRACTION1O268 - 281
4X-RAY DIFFRACTION1O285 - 354
5X-RAY DIFFRACTION1O357 - 394
6X-RAY DIFFRACTION1O405 - 455
7X-RAY DIFFRACTION1O470 - 497
8X-RAY DIFFRACTION2X5 - 227
9X-RAY DIFFRACTION2X268 - 281
10X-RAY DIFFRACTION2X285 - 354
11X-RAY DIFFRACTION2X357 - 394
12X-RAY DIFFRACTION2X405 - 455
13X-RAY DIFFRACTION2X470 - 497

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