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- PDB-1ex7: CRYSTAL STRUCTURE OF YEAST GUANYLATE KINASE IN COMPLEX WITH GUANO... -

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Basic information

Entry
Database: PDB / ID: 1ex7
TitleCRYSTAL STRUCTURE OF YEAST GUANYLATE KINASE IN COMPLEX WITH GUANOSINE-5'-MONOPHOSPHATE
ComponentsGUANYLATE KINASE
KeywordsTRANSFERASE / GUANYLATE KINASE / SUBSTRATE-INDUCED FIT / DOMAIN MOVEMENT / GMP / ATP / 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
GUANOSINE-5'-MONOPHOSPHATE / Guanylate kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / REFINEMENT OF THE MODEL / Resolution: 1.9 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 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
Revision 1.4Aug 30, 2023Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID

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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)21,0884
Polymers20,5331
Non-polymers5553
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.625, 50.625, 155.327
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: 20533.152 Da / Num. of mol.: 1
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / 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.: 208 / 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: 2.3 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulfate, sodium phosphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
pH: 7
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
210 mMTris-HCl1drop
310 mMGMP1drop
42.0 Mammonium sulfate1reservoir
550 mMsodium phosphate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54178
DetectorType: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Dec 5, 1996 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. all: 15836 / Num. obs: 15836 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 1.8455 / Num. unique all: 716 / % possible all: 86.9
Reflection
*PLUS
Num. measured all: 72765
Reflection shell
*PLUS
% possible obs: 86.9 %

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: REFINEMENT OF THE MODEL
Starting model: 1GKY

1gky


Resolution: 1.9→15 Å / Num. parameters: 6733 / Num. restraintsaints: 6051 / 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
Rfree0.257 1575 11.111 %RANDOM
Rwork0.1701 ---
obs0.1701 11611 84.7 %-
all-14174 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1975)201-228
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1688
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 0 34 208 1688
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.021
X-RAY DIFFRACTIONs_zero_chiral_vol0.035
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.044
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.085
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.1701 / Rfactor obs: 0.156
Solvent computation
*PLUS
Displacement parameters
*PLUS

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