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- PDB-1we2: Crystal structure of shikimate kinase from mycobacterium tubercul... -

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Basic information

Entry
Database: PDB / ID: 1we2
TitleCrystal structure of shikimate kinase from mycobacterium tuberculosis in complex with MGADP and shikimic acid
ComponentsShikimate kinase
KeywordsTRANSFERASE / SHIKIMATE PATHWAY / SHIKIMATE KINASE / SYNCHROTRON / DRUG DESIGN
Function / homology
Function and homology information


shikimate kinase / shikimate metabolic process / shikimate kinase activity / Chorismate via Shikimate Pathway / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / phosphorylation / 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
ADENOSINE-5'-DIPHOSPHATE / 3-DEHYDROSHIKIMATE / Shikimate kinase / Shikimate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPereira, J.H. / de Oliveira, J.S. / Canduri, F. / Dias, M.V. / Palma, M.S. / Basso, L.A. / Santos, D.S. / de Azevedo Jr., W.F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of shikimate kinase from Mycobacterium tuberculosis reveals the binding of shikimic acid.
Authors: Pereira, J.H. / de Oliveira, J.S. / Canduri, F. / Dias, M.V. / Palma, M.S. / Basso, L.A. / Santos, D.S. / de Azevedo, W.F.
History
DepositionMay 22, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3096
Polymers18,6121
Non-polymers6975
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.910, 62.910, 90.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Shikimate kinase / / SK


Mass: 18612.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: AROK / Plasmid: PET-23A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A4Z2, UniProt: P9WPY3*PLUS, shikimate kinase

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Non-polymers , 5 types, 149 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-DHK / 3-DEHYDROSHIKIMATE / 3-Dehydroshikimic acid


Mass: 174.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10O5
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: NA-HEPES, MAGNESIUM CHOLORIDE, PEG 3350, ADENOSINE-5'-DIPHOSPHATE, SHIKIMIC ACID, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.431 / Wavelength: 1.431 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 2, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.4311
21.4311
ReflectionResolution: 2.3→34.922 Å / Num. all: 34274 / Num. obs: 9563 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Rmerge(I) obs: 0.028 / Rsym value: 0.03 / Net I/σ(I): 16
Reflection shellResolution: 2.3→2.41 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.059 / Mean I/σ(I) obs: 8.3 / Rsym value: 0.072 / % possible all: 98.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L4Y

1l4y


Resolution: 2.3→6 Å / Data cutoff high absF: 2 / Data cutoff low absF: 2 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 888 10 %RANDOM
Rwork0.207 ---
all0.26 34274 --
obs0.207 8885 98.7 %-
Displacement parametersBiso mean: 35.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1226 0 42 144 1412
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg1.905
X-RAY DIFFRACTIONx_dihedral_angle_d22.125
X-RAY DIFFRACTIONx_improper_angle_d1.766

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