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- PDB-3n2e: Crystal structure of Helicobactor pylori shikimate kinase in comp... -

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Basic information

Entry
Database: PDB / ID: 3n2e
TitleCrystal structure of Helicobactor pylori shikimate kinase in complex with NSC162535
ComponentsShikimate kinase
KeywordsTRANSFERASE / alpha-beta-alpha fold
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
Chem-OSA / L(+)-TARTARIC ACID / Shikimate kinase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 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 18, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 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

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Assembly

Deposited unit
A: Shikimate kinase
B: Shikimate kinase
C: Shikimate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,74210
Polymers57,0123
Non-polymers1,7297
Water1,49583
1
A: Shikimate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7944
Polymers19,0041
Non-polymers7903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Shikimate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9445
Polymers19,0041
Non-polymers9404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Shikimate kinase


Theoretical massNumber of molelcules
Total (without water)19,0041
Polymers19,0041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)193.910, 71.791, 47.626
Angle α, β, γ (deg.)90.00, 91.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-193-

HOH

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Components

#1: Protein Shikimate kinase / SK


Mass: 19004.135 Da / Num. of mol.: 3 / Mutation: E114A
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-OSA / 7-amino-4-hydroxy-3-[(E)-(5-hydroxy-7-sulfonaphthalen-2-yl)diazenyl]naphthalene-2-sulfonic acid


Mass: 489.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H15N3O8S2
#3: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.91 Å3/Da / Density % sol: 57.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 0.1M sodium HEPES, 1.2M potassium sodium tartrate tetrahydrate, pH 6.7, 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: 2.53→30 Å / Num. all: 21908 / Num. obs: 21900 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 26.88
Reflection shellResolution: 2.53→2.62 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 4.33 / Num. unique all: 2150 / Rsym value: 0.305 / % possible all: 98.3

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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 1ZUH

1zuh


Resolution: 2.53→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.915 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26309 1101 5 %RANDOM
Rwork0.21703 ---
obs0.21933 20807 99.49 %-
all-20900 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.303 Å2
Baniso -1Baniso -2Baniso -3
1--3.29 Å20 Å2-0.75 Å2
2---0.41 Å20 Å2
3---3.65 Å2
Refinement stepCycle: LAST / Resolution: 2.53→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3661 0 116 83 3860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223821
X-RAY DIFFRACTIONr_angle_refined_deg2.0182.0215131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5015460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.32825.092163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.13715752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.031520
X-RAY DIFFRACTIONr_chiral_restr0.1360.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022759
X-RAY DIFFRACTIONr_mcbond_it0.9641.52284
X-RAY DIFFRACTIONr_mcangle_it1.8923657
X-RAY DIFFRACTIONr_scbond_it3.04731537
X-RAY DIFFRACTIONr_scangle_it4.994.51474
LS refinement shellResolution: 2.528→2.593 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 95 -
Rwork0.281 1425 -
obs--95.48 %

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