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- PDB-1zuh: Structural Basis for Shikimate-binding Specificity of Helicobacte... -

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Basic information

Entry
Database: PDB / ID: 1zuh
TitleStructural Basis for Shikimate-binding Specificity of Helicobacter pylori Shikimate Kinase
ComponentsShikimate kinase
KeywordsTRANSFERASE / alpha-beta protein
Function / homology
Function and homology information


shikimate kinase / shikimate kinase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / phosphorylation / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCheng, W.C. / Chang, Y.N. / Wang, W.C.
CitationJournal: J.Bacteriol. / Year: 2005
Title: Structural basis for shikimate-binding specificity of Helicobacter pylori shikimate kinase
Authors: Cheng, W.C. / Chang, Y.N. / Wang, W.C.
History
DepositionMay 31, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 25, 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)19,2651
Polymers19,2651
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.494, 94.494, 39.299
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-319-

HOH

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Components

#1: Protein Shikimate kinase


Mass: 19265.336 Da / Num. of mol.: 1
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.: 165 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: lithium sulfate,PEG 8000, sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→67.42 Å / Num. all: 17391 / Num. obs: 17190 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.6 % / Rmerge(I) obs: 0.043 / Χ2: 0.998
Reflection shellResolution: 1.79→1.85 Å / % possible obs: 90.1 % / Redundancy: 11 % / Rmerge(I) obs: 0.395 / Num. measured obs: 1519 / Χ2: 0.974 / % possible all: 89.9

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Phasing

Phasing MRRfactor: 0.4 / Cor.coef. Fo:Fc: 0.614
Highest resolutionLowest resolution
Rotation3 Å23.79 Å
Translation3 Å23.79 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT1.601data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VIA

1via


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.63 / SU ML: 0.084 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.136 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.266 867 5.1 %RANDOM
Rwork0.21 ---
all0.223 17391 --
obs0.213 16283 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.549 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1198 0 0 165 1363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221211
X-RAY DIFFRACTIONr_angle_refined_deg1.9921.9841620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945149
X-RAY DIFFRACTIONr_chiral_restr0.3220.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02871
X-RAY DIFFRACTIONr_nbd_refined0.240.2588
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4090.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.215
X-RAY DIFFRACTIONr_mcbond_it1.2331.5741
X-RAY DIFFRACTIONr_mcangle_it2.35321185
X-RAY DIFFRACTIONr_scbond_it3.6383470
X-RAY DIFFRACTIONr_scangle_it5.9144.5435
LS refinement shellResolution: 1.795→1.842 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.254 61
Rwork0.224 1167

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