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- PDB-3mrs: Crystal structure of shikimate kinase mutant (R57A) from Helicoba... -

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Basic information

Entry
Database: PDB / ID: 3mrs
TitleCrystal structure of shikimate kinase mutant (R57A) from Helicobacter pylori
ComponentsShikimate kinase
KeywordsTRANSFERASE / helix-sheet complex
Function / homology
Function and homology information


shikimate kinase / shikimate kinase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Shikimate kinase, conserved site / Shikimate kinase signature. / Shikimate kinase/Threonine synthase-like 1 / Shikimate kinase/gluconokinase / Shikimate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCheng, W.C. / Chen, T.J. / Lin, S.C. / Wang, W.C.
CitationJournal: Plos One / Year: 2012
Title: Structures of Helicobacter pylori shikimate kinase reveal a selective inhibitor-induced-fit mechanism
Authors: Cheng, W.C. / Chen, Y.F. / Wang, H.J. / Hsu, K.C. / Lin, S.C. / Chen, T.J. / Yang, J.M. / Wang, W.C.
History
DepositionApr 29, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 30, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Shikimate kinase


Theoretical massNumber of molelcules
Total (without water)19,1791
Polymers19,1791
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.899, 88.899, 39.874
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 Shikimate kinase / SK


Mass: 19179.221 Da / Num. of mol.: 1 / Mutation: R57A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: AROK / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P56073, shikimate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18% PEG 4000, 8% isopropanol, 0.1M sodium HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 6651 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.4 % / Biso Wilson estimate: 44.2 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 56.02
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.131 / Mean I/σ(I) obs: 19.49 / Num. unique all: 1222 / Rsym value: 0.131 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZUI

1zui


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.869 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.537 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27277 341 5.1 %RANDOM
Rwork0.24597 ---
all0.24737 6287 --
obs0.24737 6287 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 0 25 1197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221185
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.991585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7695147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.16225.29451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.56415240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.011155
X-RAY DIFFRACTIONr_chiral_restr0.1250.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02842
X-RAY DIFFRACTIONr_mcbond_it1.1931.5731
X-RAY DIFFRACTIONr_mcangle_it1.95321168
X-RAY DIFFRACTIONr_scbond_it2.4733454
X-RAY DIFFRACTIONr_scangle_it4.1094.5417
LS refinement shellResolution: 2.399→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 23 -
Rwork0.22 437 -
obs--98.5 %

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