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- PDB-1ex6: CRYSTAL STRUCTURE OF UNLIGANDED FORM OF GUANYLATE KINASE FROM YEAST -

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Basic information

Entry
Database: PDB / ID: 1ex6
TitleCRYSTAL STRUCTURE OF UNLIGANDED FORM OF GUANYLATE KINASE FROM YEAST
ComponentsGUANYLATE KINASE
KeywordsTRANSFERASE / GUANYLATE KINASE / SUBSTRATE-INDUCED FIT / DOMAIN MOVEMENT / ATP / GMP / SUBSTRATE SPECIFICITY
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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / HGMAD / Resolution: 2.3 Å
AuthorsBlaszczyk, J. / Ji, X.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of unligated guanylate kinase from yeast reveals GMP-induced conformational changes.
Authors: Blaszczyk, J. / Li, Y. / Yan, H. / Ji, X.
History
DepositionMay 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GUANYLATE KINASE
B: GUANYLATE KINASE


Theoretical massNumber of molelcules
Total (without water)41,0662
Polymers41,0662
Non-polymers00
Water7,638424
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.559, 51.559, 119.645
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein GUANYLATE KINASE


Mass: 20533.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PET17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15454, guanylate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.1 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, Tris-HCl, acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 100 K / pH: 7
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
210 mMTris-HCl1drop
330 %(w/v)PEG40001reservoir
40.3 Msodium acetate1reservoir
50.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.92
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 24, 1998 / Details: MIRROR
RadiationMonochromator: SILICON 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 15759 / Num. obs: 15759 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.37 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.9917
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.13 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 1.5845 / Num. unique all: 776 / % possible all: 97.9
Reflection
*PLUS
Num. measured all: 37285
Reflection shell
*PLUS
% possible obs: 97.9 %

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Processing

Software
NameClassification
SOLVEphasing
PHASESphasing
DMmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: HGMAD / Resolution: 2.3→20 Å / Num. parameters: 11965 / Num. restraintsaints: 11875 / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER
Details: Least-squares refinement using the Konnert-Hendrickson conjugate-gradient algorithm
RfactorNum. reflection% reflectionSelection details
Rfree0.259 797 -RANDOM
Rwork0.1754 ---
obs0.214 11353 94.7 %-
all-14941 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1975)201-228
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3306
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 0 424 3316
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.017
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.02
X-RAY DIFFRACTIONs_zero_chiral_vol0.019
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.025
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.087
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.214 / Rfactor obs: 0.164
Solvent computation
*PLUS
Displacement parameters
*PLUS

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