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- PDB-1gky: REFINED STRUCTURE OF THE COMPLEX BETWEEN GUANYLATE KINASE AND ITS... -

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Basic information

Entry
Database: PDB / ID: 1gky
TitleREFINED STRUCTURE OF THE COMPLEX BETWEEN GUANYLATE KINASE AND ITS SUBSTRATE GMP AT 2.0 ANGSTROMS RESOLUTION
ComponentsGUANYLATE KINASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


Azathioprine ADME / GDP biosynthetic process / guanylate kinase / purine nucleotide metabolic process / Interconversion of nucleotide di- and triphosphates / GMP kinase activity / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / Guanylate kinase / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. ...Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / Guanylate kinase / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / Guanylate kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsStehle, T. / Schulz, G.E.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Refined structure of the complex between guanylate kinase and its substrate GMP at 2.0 A resolution.
Authors: Stehle, T. / Schulz, G.E.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Three-Dimensional Structure of the Complex of Guanylate Kinase from Yeast with its Substrate Gmp
Authors: Stehle, T. / Schulz, G.E.
#2: Journal: Eur.J.Biochem. / Year: 1989
Title: Guanylate Kinase from Saccharomyces Cerevisiae. Isolation and Characterization, Crystallization and Preliminary X-Ray Analysis, Amino Acid Sequence and Comparison with Adenylate Kinases
Authors: Berger, A. / Schiltz, E. / Schulz, G.E.
History
DepositionDec 23, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GUANYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0183
Polymers20,5591
Non-polymers4592
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.800, 50.800, 155.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein GUANYLATE KINASE


Mass: 20559.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P15454, guanylate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlGK1drop
240 mMpotassium phosphate1drop
31 mMGMP1drop
41 %(w/v)PEG15001drop
51.0 Mammonium sulfate1drop
640 mMpotassium phosphate1reservoir
72.0 Mammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 14130 / % possible obs: 100 % / Rmerge(I) obs: 0.05

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Processing

SoftwareName: SIMULATED / Version: ANNEALING METHOD / Classification: refinement
RefinementRfactor Rwork: 0.173 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1449 0 29 173 1651
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.016
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg3
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 7 Å / Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_d3
X-RAY DIFFRACTIONo_dihedral_angle_d23.7
X-RAY DIFFRACTIONo_dihedral_angle_deg1.4

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