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- PDB-1bot: CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN ESCHERICHIA COLI GLYCERO... -

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Basic information

Entry
Database: PDB / ID: 1bot
TitleCRYSTAL STRUCTURE OF THE COMPLEX BETWEEN ESCHERICHIA COLI GLYCEROL KINASE AND THE ALLOSTERIC REGULATOR FRUCTOSE 1,6-BISPHOSPHATE.
ComponentsPROTEIN (GLYCEROL KINASE)
KeywordsTRANSFERASE / KINASE / ALLOSTERIC REGULATION / FRUCTOSE BISPHOSPHATE
Function / homology
Function and homology information


glycerol-3-phosphate metabolic process / glycerol kinase / glycerol kinase activity / glycerol metabolic process / glycerol catabolic process / DNA damage response / zinc ion binding / ATP binding / identical protein binding / metal ion 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsOrmo, M. / Bystrom, C.E. / Remington, S.J.
CitationJournal: Biochemistry / Year: 1998
Title: Crystal structure of a complex of Escherichia coli glycerol kinase and an allosteric effector fructose 1,6-bisphosphate.
Authors: Ormo, M. / Bystrom, C.E. / Remington, S.J.
History
DepositionAug 5, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
O: PROTEIN (GLYCEROL KINASE)
Z: PROTEIN (GLYCEROL KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,7475
Polymers112,3252
Non-polymers4223
Water00
1
O: PROTEIN (GLYCEROL KINASE)
hetero molecules

O: PROTEIN (GLYCEROL KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9866
Polymers112,3252
Non-polymers6614
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4030 Å2
ΔGint-13 kcal/mol
Surface area32480 Å2
MethodPISA, PQS
2
Z: PROTEIN (GLYCEROL KINASE)
hetero molecules

Z: PROTEIN (GLYCEROL KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,5094
Polymers112,3252
Non-polymers1842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4070 Å2
ΔGint-12 kcal/mol
Surface area33920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)168.800, 168.800, 202.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.68994, -0.311658, -0.653338), (-0.325823, -0.672259, 0.664761), (-0.646391, 0.671518, 0.362273)
Vector: 155.99388, 22.12158, 63.89221)

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Components

#1: Protein PROTEIN (GLYCEROL KINASE)


Mass: 56162.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: GKWT(PET28B) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6F3, glycerol kinase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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: 1

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Sample preparation

CrystalDensity Matthews: 6.4 Å3/Da / Density % sol: 81 %
Crystal growpH: 7.5
Details: 1M SODIUM CITRATE, 0.1M HEPES PH 7.5, 1MM BME, CRYO PROTECTION WAS ACHIEVED BY SOAKING CRYSTAL IN MOTHER LIQUOR CONTAINING 20% GLYCEROL FOR 4 HOURS
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 Msodium citrate1reservoir
20.1 MHEPES1reservoir
31 mMbeta-mercaptoethanol1reservoir
412 mg/mlprotein1drop
510 mMglycerol1drop
61 mMEDTA1drop
72 mMbeta-mercaptoethanol1drop
820 mMHEPES1drop

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Data collection

DiffractionMean temperature: 102 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 15, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.05→20 Å / Num. obs: 45656 / % possible obs: 81 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.09

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Processing

Software
NameVersionClassification
TNT5Frefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GLA

1gla


Resolution: 3.05→20 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.219 --
all-174719 -
obs-48098 81 %
Solvent computationBsol: 300 Å2 / ksol: 0.75 e/Å3
Refinement stepCycle: LAST / Resolution: 3.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7837 0 27 0 7864
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01680223
X-RAY DIFFRACTIONt_angle_deg2.56396496
X-RAY DIFFRACTIONt_dihedral_angle_d21.07147860
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0152094
X-RAY DIFFRACTIONt_gen_planes0.012117120
X-RAY DIFFRACTIONt_it3.755799710
X-RAY DIFFRACTIONt_nbd0.02436735
Software
*PLUS
Name: TNT / Version: 5F / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg21.0710
X-RAY DIFFRACTIONt_plane_restr0.01220

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