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- PDB-1kag: Crystal Structure of the Escherichia coli Shikimate Kinase I (AroK) -

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Basic information

Entry
Database: PDB / ID: 1kag
TitleCrystal Structure of the Escherichia coli Shikimate Kinase I (AroK)
ComponentsShikimate kinase I
KeywordsTRANSFERASE / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


shikimate kinase / shikimate metabolic process / shikimate kinase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / response to antibiotic / 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsRomanowski, M.J. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proteins / Year: 2002
Title: Crystal structure of the Escherichia coli shikimate kinase I (AroK) that confers sensitivity to mecillinam.
Authors: Romanowski, M.J. / Burley, S.K.
History
DepositionNov 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Refinement description / Structure summary
Category: audit_author / citation_author / software
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _software.classification / _software.name / _software.version
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Shikimate kinase I
B: Shikimate kinase I


Theoretical massNumber of molelcules
Total (without water)39,1302
Polymers39,1302
Non-polymers00
Water4,648258
1
A: Shikimate kinase I


Theoretical massNumber of molelcules
Total (without water)19,5651
Polymers19,5651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Shikimate kinase I


Theoretical massNumber of molelcules
Total (without water)19,5651
Polymers19,5651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.726, 63.417, 67.941
Angle α, β, γ (deg.)90.00, 91.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Shikimate kinase I / SKI


Mass: 19565.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: AROK / Plasmid: pGEX6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A6D7, shikimate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 1.97 Å3/Da / Density % sol: 37.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 5000 MME, 0.2M ammonium sulfate, 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 MMES1reservoirpH6.5
20.2 Mammonium sulfate1reservoir
330 %PEG5000 MME1reservoir
420 mMHEPES1droppH7.5
5100 mM1dropKCl
63 mMdithiothreitol1drop
710 mg/mlprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X9A10.97962
SYNCHROTRONNSLS X9A20.98167, 0.98147
Detector
TypeIDDetectorDate
MARRESEARCH1CCDAug 3, 2001
MARRESEARCH2CCDOct 21, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2Si 111MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979621
20.981671
30.981471
ReflectionResolution: 2.05→20 Å / Num. all: 19149 / Num. obs: 19149 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.031
Reflection shellResolution: 2.03→2.13 Å / Rmerge(I) obs: 0.049 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 19142 / Rmerge(I) obs: 0.031
Reflection shell
*PLUS
Rmerge(I) obs: 0.049

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Processing

Software
NameVersionClassification
SnBphasing
MLPHAREphasing
DMmodel building
CNS1refinement
MARMADdata reduction
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→19.58 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 769059.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1874 10 %RANDOM
Rwork0.217 ---
all0.2216 18666 --
obs0.217 18666 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.2088 Å2 / ksol: 0.405494 e/Å3
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.41 Å20 Å20.58 Å2
2--1.41 Å20 Å2
3----3.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å-0.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2414 0 0 258 2672
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it3.591.5
X-RAY DIFFRACTIONc_mcangle_it4.372
X-RAY DIFFRACTIONc_scbond_it5.422
X-RAY DIFFRACTIONc_scangle_it7.082.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 342 10.8 %
Rwork0.195 2823 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 9.8 % / Rfactor all: 0.2216 / Rfactor obs: 0.217 / Rfactor Rfree: 0.271 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
LS refinement shell
*PLUS
Rfactor Rfree: 0.279 / Rfactor Rwork: 0.195 / Rfactor obs: 0.195

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