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- PDB-2pt5: Crystal Structure Of Shikimate Kinase (aq_2177) From Aquifex Aeol... -

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Basic information

Entry
Database: PDB / ID: 2pt5
TitleCrystal Structure Of Shikimate Kinase (aq_2177) From Aquifex Aeolicus vf5
ComponentsShikimate kinase
KeywordsTRANSFERASE / Aromatic amino acid biosynthesis / Kinase / P-loop kinase / Shikimate kinase / Shikimate pathway / Nucleotide-binding / amino-acid biosynthesis / National project on protein structural and functional analyses / ATP-binding / Magnesium / Metal-binding / Structural Genomics / NPPSFA / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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
DI(HYDROXYETHYL)ETHER / Shikimate kinase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJeyakanthan, J. / Nithya, N. / Shimada, A. / Velmurugan, D. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Shiro, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure Of Shikimate Kinase (aq_2177) From Aquifex Aeolicus vf5
Authors: Jeyakanthan, J. / Nithya, N. / Shimada, A. / Velmurugan, D. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Shiro, Y. / Yokoyama, S.
History
DepositionMay 8, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,1636
Polymers76,9954
Non-polymers1682
Water4,720262
1
A: Shikimate kinase


Theoretical massNumber of molelcules
Total (without water)19,2491
Polymers19,2491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Shikimate kinase


Theoretical massNumber of molelcules
Total (without water)19,2491
Polymers19,2491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Shikimate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4173
Polymers19,2491
Non-polymers1682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Shikimate kinase


Theoretical massNumber of molelcules
Total (without water)19,2491
Polymers19,2491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: Shikimate kinase

D: Shikimate kinase


Theoretical massNumber of molelcules
Total (without water)38,4982
Polymers38,4982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_645x+1,y-1,z1
Buried area1570 Å2
ΔGint-12 kcal/mol
Surface area15900 Å2
MethodPISA
6
A: Shikimate kinase


Theoretical massNumber of molelcules
Total (without water)19,2491
Polymers19,2491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
C: Shikimate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4173
Polymers19,2491
Non-polymers1682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.598, 57.932, 97.143
Angle α, β, γ (deg.)90.00, 90.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Shikimate kinase / SK


Mass: 19248.783 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aroK / Plasmid: pET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 CONDON PLUS (DE3)-RIL-X / References: UniProt: O67925, shikimate kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.89 Å3/Da / Density % sol: 34.77 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 4.8
Details: 27.5% PEG 4000, 0.1M Acetate-NaOH, 10% Dioxane, pH4.8, microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9790, 0.97943, 0.9000
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 17, 2006 / Details: RH Coated Bent-Cyrindrical MIRROR
RadiationMonochromator: SI 1 1 1 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979431
30.91
ReflectionResolution: 2.1→50 Å / Num. obs: 33586 / % possible obs: 99.6 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.079
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.306 / Num. unique all: 3300 / Rsym value: 0.336 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→38.53 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1609783.66 / 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
Rfree0.269 1612 4.9 %RANDOM
Rwork0.214 ---
obs0.214 32667 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.9935 Å2 / ksol: 0.328971 e/Å3
Displacement parametersBiso mean: 49.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.84 Å20 Å22.47 Å2
2---2.72 Å20 Å2
3---7.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.1→38.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5180 0 11 262 5453
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.348 209 5.5 %
Rwork0.274 3579 -
obs--91.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ligand.parligand.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION5water_rep.paramwater_protin.top

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