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- PDB-1via: Crystal structure of shikimate kinase -

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Basic information

Entry
Database: PDB / ID: 1via
TitleCrystal structure of shikimate kinase
Componentsshikimate kinase
KeywordsTRANSFERASE / structural genomics
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 / cytoplasm
Similarity search - Function
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
Shikimate kinase / :
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsStructural GenomiX
CitationJournal: Proteins / Year: 2005
Title: Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J.
History
DepositionDec 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
B: shikimate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3145
Polymers41,0262
Non-polymers2883
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-59 kcal/mol
Surface area15410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.931, 43.230, 52.606
Angle α, β, γ (deg.)81.51, 76.58, 77.87
Int Tables number1
Space group name H-MP1

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Components

#1: Protein shikimate kinase /


Mass: 20513.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: aroK / Production host: Escherichia coli (E. coli)
References: UniProt: Q9PIB5, UniProt: Q0PBC3*PLUS, shikimate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.5
2150 mM1dropNaCl
310 mMmethionine1drop
410 %glycerol1drop
55 mMdithiothreitol1drop
610 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.56→24.56 Å / Num. all: 48564 / Num. obs: 48564 / % possible obs: 98 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.6
Reflection shellResolution: 1.56→1.65 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 2.8 / % possible all: 86.4
Reflection
*PLUS
Highest resolution: 1.57 Å
Reflection shell
*PLUS
% possible obs: 86.4 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
REFMAC4refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→24.56 Å / σ(F): 0
RfactorNum. reflection
Rfree0.228 2427
Rwork0.198 -
obs-48563
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 180.597 Å2 / ksol: 0.762 e/Å3
Displacement parametersBiso mean: 24.755 Å2
Baniso -1Baniso -2Baniso -3
1-1.361 Å2-1.061 Å2-1.444 Å2
2---0.255 Å21.509 Å2
3----0.436 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 1.57→24.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2561 0 15 350 2926
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d1.736
X-RAY DIFFRACTIONp_planar_tor3.19
X-RAY DIFFRACTIONp_chiral_restr0.114
X-RAY DIFFRACTIONp_plane_restr0.01
X-RAY DIFFRACTIONp_mcbond_it1.704
X-RAY DIFFRACTIONp_mcangle_it3.028
X-RAY DIFFRACTIONp_scbond_it2.945
X-RAY DIFFRACTIONp_scangle_it4.674
Software
*PLUS
Version: 4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.7

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