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- PDB-3muf: Shikimate kinase from Helicobacter pylori in complex with shikima... -

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Basic information

Entry
Database: PDB / ID: 3muf
TitleShikimate kinase from Helicobacter pylori in complex with shikimate-3-phosphate and ADP
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
ADENOSINE-5'-DIPHOSPHATE / SHIKIMATE-3-PHOSPHATE / Shikimate kinase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionMay 3, 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 ...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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Shikimate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9473
Polymers19,2651
Non-polymers6812
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.816, 98.816, 42.129
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Shikimate kinase / SK


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: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-S3P / SHIKIMATE-3-PHOSPHATE


Mass: 254.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.22 Å3/Da / Density % sol: 61.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% PEG 8000, 0.1M sodium acetate, 0.1M HEPES, 2% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 10585 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.7 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 29.28
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.47 / Num. unique all: 2011 / Rsym value: 0.488 / % possible all: 99.5

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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: 2.3→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27694 537 5.1 %RANDOM
Rwork0.23126 ---
all0.2335 10003 --
obs0.2335 10003 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.19 Å2
Baniso -1Baniso -2Baniso -3
1--6 Å2-3 Å20 Å2
2---6 Å20 Å2
3---9 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1279 0 43 59 1381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221339
X-RAY DIFFRACTIONr_angle_refined_deg1.782.0311800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3725159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6032560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.48815267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.003158
X-RAY DIFFRACTIONr_chiral_restr0.1170.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02951
X-RAY DIFFRACTIONr_mcbond_it0.9231.5788
X-RAY DIFFRACTIONr_mcangle_it1.75721264
X-RAY DIFFRACTIONr_scbond_it2.6493551
X-RAY DIFFRACTIONr_scangle_it4.2994.5536
LS refinement shellResolution: 2.304→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.486 38 -
Rwork0.409 727 -
obs--99.09 %

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