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- PDB-1bwf: ESCHERICHIA COLI GLYCEROL KINASE MUTANT WITH BOUND ATP ANALOG SHO... -

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Basic information

Entry
Database: PDB / ID: 1bwf
TitleESCHERICHIA COLI GLYCEROL KINASE MUTANT WITH BOUND ATP ANALOG SHOWING SUBSTANTIAL DOMAIN MOTION
ComponentsGLYCEROL KINASE
KeywordsTRANSFERASE / KINASE / DOMAIN MOTION / ALLOSTERIC REGULATION HYDROLASE / LIPID DEGRADATION / PLATELET FACTOR
Function / homology
Function and homology information


glycerol kinase / glycerol kinase activity / glycerol-3-phosphate metabolic process / glycerol metabolic process / glycerol catabolic process / phosphorylation / DNA damage response / zinc ion binding / ATP binding / metal ion binding ...glycerol kinase / glycerol kinase activity / glycerol-3-phosphate metabolic process / glycerol metabolic process / glycerol catabolic process / phosphorylation / DNA damage response / zinc ion binding / ATP binding / metal ion binding / identical protein 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
Chem-ATF / Glycerol kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBystrom, C.E. / Pettigrew, D.W. / Branchaud, B.P. / Remington, S.J.
CitationJournal: Biochemistry / Year: 1999
Title: Crystal structures of Escherichia coli glycerol kinase variant S58-->W in complex with nonhydrolyzable ATP analogues reveal a putative active conformation of the enzyme as a result of domain motion.
Authors: Bystrom, C.E. / Pettigrew, D.W. / Branchaud, B.P. / O'Brien, P. / Remington, S.J.
History
DepositionSep 23, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: GLYCEROL KINASE
O: GLYCEROL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8388
Polymers112,5232
Non-polymers1,3156
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-32 kcal/mol
Surface area33640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.767, 200.293, 114.738
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.234307, -0.09614, 0.967397), (0.076516, -0.990187, -0.116937), (0.969147, 0.101421, -0.224652)16.24312, 63.53759, -15.88193
2given(0.268558, -0.000483, 0.963263), (0.056162, -0.998291, -0.016159), (0.961625, 0.058439, -0.268072)9.07226, 64.60217, -13.38748

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Components

#1: Protein GLYCEROL KINASE /


Mass: 56261.484 Da / Num. of mol.: 2 / Mutation: S58W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Tissue: PLATELET / Description: CLONED GENE / Organ: SEED / Gene (production host): GLPK / Production host: Escherichia coli (E. coli) / Strain (production host): DG1 (DE3) / References: UniProt: P0A6F3, glycerol kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATF / PHOSPHODIFLUOROMETHYLPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 541.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16F2N5O12P3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.4 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlenzyme1drop
28.3 %PEG10001drop
30.13 M1dropMgCl2
40.04 MPIPES1drop
50.08 M1dropNaCl
68.3 mMinhibitor1drop
720 %PEG10001reservoir
80.3 M1reservoirMgCl2
90.1 MPIPES1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jun 1, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 22234 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.061
Reflection
*PLUS
Num. obs: 24796 / Num. measured all: 84144 / Rmerge(I) obs: 0.071

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Processing

Software
NameVersionClassification
TNT5Frefinement
SDMSdata reduction
SDMSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GLJ

1glj


Resolution: 3→20 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: DUE TO LIMITED RESOLUTION OF THE DIFFRACTION DATA NO SOLVENT MOLECULES WERE ADDED TO THE STRUCTURE. ONE MAGNESIUM ATOM WAS ADDED BASED ON MANGANESE SOAKING EXPERIMENTS. RESIDUES IN ...Details: DUE TO LIMITED RESOLUTION OF THE DIFFRACTION DATA NO SOLVENT MOLECULES WERE ADDED TO THE STRUCTURE. ONE MAGNESIUM ATOM WAS ADDED BASED ON MANGANESE SOAKING EXPERIMENTS. RESIDUES IN DISALLOWED REGIONS OF THE RAMACHANDRAN PLOT ARE ASSOCIATED WITH REGIONS OF POOR ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rwork0.168 --
all0.168 2234 -
obs-22234 95 %
Solvent computationSolvent model: TNT SOLVENT MODEL / Bsol: 200 Å2 / ksol: 0.7 e/Å3
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7820 0 80 0 7900
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01880801.7
X-RAY DIFFRACTIONt_angle_deg2.93597463.1
X-RAY DIFFRACTIONt_dihedral_angle_d21.8147680
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0192122
X-RAY DIFFRACTIONt_gen_planes0.01811628
X-RAY DIFFRACTIONt_it3.79980006
X-RAY DIFFRACTIONt_nbd0.01435750
Software
*PLUS
Name: TNT / Version: 5F / Classification: refinement
Refinement
*PLUS
Num. reflection all: 22234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg21.810
X-RAY DIFFRACTIONt_planar_d0.0192
X-RAY DIFFRACTIONt_plane_restr0.0188

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