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- PDB-1z8f: Guanylate Kinase Double Mutant A58C, T157C from Mycobacterium tub... -

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Basic information

Entry
Database: PDB / ID: 1z8f
TitleGuanylate Kinase Double Mutant A58C, T157C from Mycobacterium tuberculosis (Rv1389)
ComponentsGuanylate kinase
KeywordsTRANSFERASE / ATP:GMP-PHOSPHOTRANSFERASE / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / TB STRUCTURAL GENOMICS CONSORTIUM / TBSGC / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB
Function / homology
Function and homology information


GMP binding / guanylate kinase / guanylate kinase activity / adenylate kinase activity / GDP binding / phosphorylation / magnesium ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Guanylate kinase / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / 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 / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Guanylate kinase / Guanylate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Difference Fourier Map / Resolution: 2.5 Å
AuthorsChan, S. / Sawaya, M.R. / Choi, B. / Zocchi, G. / Perry, L.J. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)
CitationJournal: To be Published
Title: Crystal Structure of Guanylate Kinase from Mycobacterium tuberculosis (Rv1389)
Authors: Chan, S. / Sawaya, M.R. / Choi, B. / Zocchi, G. / Perry, L.J.
History
DepositionMar 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)24,4133
Polymers24,3211
Non-polymers922
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.306, 112.306, 112.306
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Guanylate kinase / / GMP kinase


Mass: 24320.824 Da / Num. of mol.: 1 / Mutation: A58C,T157C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: gmk / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3)
References: UniProt: P0A5I4, UniProt: P9WKE9*PLUS, guanylate kinase
#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.6M sodium formate, 2% glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2004
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→90 Å / Num. all: 8301 / Num. obs: 8301 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rsym value: 0.042 / Net I/σ(I): 35.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 807 / Rsym value: 0.446 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
Blu-Icedata collection
SCALEPACKdata scaling
RefinementMethod to determine structure: Difference Fourier Map
Starting model: 1S4Q

1s4q


Resolution: 2.5→79.31 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.924 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23576 375 4.5 %RANDOM
Rwork0.18061 ---
all0.18314 7909 --
obs0.18314 7909 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.517 Å2
Refinement stepCycle: LAST / Resolution: 2.5→79.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1394 0 6 22 1422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221423
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9711933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2075183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5822.33360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66915233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0771517
X-RAY DIFFRACTIONr_chiral_restr0.0880.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021072
X-RAY DIFFRACTIONr_nbd_refined0.210.2605
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2989
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.252
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.23
X-RAY DIFFRACTIONr_mcbond_it1.351.5936
X-RAY DIFFRACTIONr_mcangle_it1.4721476
X-RAY DIFFRACTIONr_scbond_it2.7323530
X-RAY DIFFRACTIONr_scangle_it4.6914.5457
LS refinement shellResolution: 2.5→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 18 -
Rwork0.273 578 -
obs--97.23 %
Refinement TLS params.Method: refined / Origin x: 5.5098 Å / Origin y: 37.1557 Å / Origin z: 19.9592 Å
111213212223313233
T0.0243 Å20.0399 Å2-0.0358 Å2--0.0465 Å2-0.0407 Å2--0.0382 Å2
L2.0308 °20.1009 °2-0.544 °2-0.9081 °2-0.5438 °2--1.1842 °2
S0.0385 Å °0.0847 Å °0.0288 Å °-0.0904 Å °0.1019 Å °0.0108 Å °0.157 Å °-0.0462 Å °-0.1404 Å °

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