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- PDB-1bo5: CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN ESCHERICHIA COLI GLYCERO... -

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Basic information

Entry
Database: PDB / ID: 1bo5
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 / 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
1,6-di-O-phosphono-beta-D-fructofuranose / Glycerol kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 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 10, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)112,8495
Polymers112,3252
Non-polymers5243
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
O: PROTEIN (GLYCEROL KINASE)
Z: PROTEIN (GLYCEROL KINASE)
hetero molecules

O: PROTEIN (GLYCEROL KINASE)
Z: PROTEIN (GLYCEROL KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,69810
Polymers224,6494
Non-polymers1,0496
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area12930 Å2
ΔGint-35 kcal/mol
Surface area60630 Å2
MethodPISA
3
O: PROTEIN (GLYCEROL KINASE)
hetero molecules

O: PROTEIN (GLYCEROL KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,1896
Polymers112,3252
Non-polymers8644
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
MethodPQS
4
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
MethodPQS
Unit cell
Length a, b, c (Å)169.410, 169.410, 204.676
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: (-0.700883, -0.301685, -0.646335), (-0.311927, -0.685268, 0.65811), (-0.641455, 0.662867, 0.386189)
Vector: 155.62241, 21.92773, 62.25621)

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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: Sugar ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#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: PROTEIN CRYSTALLIZED FROM LIQUOR CONTAINING 1 M SODIUM CITRATE, 0.1 M HEPES PH 7.5, 1 MM BME. CRYO PROTECTION WAS ACHIEVED BY SOAKING CRYSTAL IN MOTHER LIQUOR CONTAINING 20% GLYCEROL FOR 4 ...Details: PROTEIN CRYSTALLIZED FROM LIQUOR CONTAINING 1 M SODIUM CITRATE, 0.1 M HEPES PH 7.5, 1 MM BME. CRYO PROTECTION WAS ACHIEVED BY SOAKING CRYSTAL IN MOTHER LIQUOR CONTAINING 20% GLYCEROL FOR 4 HOURS. 20 MM FBP WAS ADDED TO THE CRYO PROTECTION IN THE SOAKING EXPERIMENT
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
210 mMglycerol1drop
31 mMEDTA1drop
42 mMbeta-mercaptoethanol1drop
520 mMHEPES1drop
61 Msodium citrate1reservoir
70.1 MHEPES1reservoir
81 mMbeta-mercaptoethanol1reservoir

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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: May 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: 3.2→20 Å / Num. obs: 54096 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.092
Reflection
*PLUS
Num. measured all: 188539

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Processing

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

1gla


Resolution: 3.2→20 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.211 --
all-54096 -
obs-54096 94 %
Solvent computationBsol: 300 Å2 / ksol: 0.75 e/Å3
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7766 0 32 0 7798
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01679763
X-RAY DIFFRACTIONt_angle_deg2.505108026
X-RAY DIFFRACTIONt_dihedral_angle_d20.92447240
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0142044
X-RAY DIFFRACTIONt_gen_planes0.016116013
X-RAY DIFFRACTIONt_it3.391792610
X-RAY DIFFRACTIONt_nbd0.02327735
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_deg20.9240
X-RAY DIFFRACTIONt_plane_restr0.01613

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