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- PDB-3baf: Crystal structure of shikimate kinase from Mycobacterium tubercul... -

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Basic information

Entry
Database: PDB / ID: 3baf
TitleCrystal structure of shikimate kinase from Mycobacterium tuberculosis in complex with AMP-PNP
ComponentsShikimate kinase
KeywordsTRANSFERASE / shikimate kinase / shikimate pathway / AMP-PNP / Amino-acid biosynthesis / Aromatic amino acid biosynthesis / ATP-binding / Cytoplasm / Magnesium / Metal-binding / Nucleotide-binding
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-SKM / Shikimate kinase / Shikimate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsFaim, L.M. / Dias, M.V.B. / Vasconcelos, I.G. / Basso, L.A. / Santos, D.S. / Azevedo, W.F. / Ruggiero, N.J.
CitationJournal: To be Published
Title: Crystal Structure for shikimate kinase from Mycobacterium tuberculosis in complex with AMP-PNP
Authors: Faim, L.M. / Dias, M.V.B. / Vasconcelos, I.G. / Basso, L.A. / Santos, D.S. / Azevedo, W.F. / Ruggiero, N.J.
History
DepositionNov 7, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)19,2933
Polymers18,6121
Non-polymers6802
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.297, 67.297, 97.692
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#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: pET23a / Production host: Escherichia coli (E. coli)
References: UniProt: P0A4Z2, UniProt: P9WPY3*PLUS, shikimate kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-SKM / (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID / SHIKIMATE / Shikimic acid


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


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.43 Å3/Da / Density % sol: 64.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: PEG, pH8, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 17, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 2.25→37.42 Å / Num. obs: 12600 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.19 / Rsym value: 0.13 / Net I/σ(I): 25.8
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.19 / Num. unique all: 1816 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZYU
Resolution: 2.25→37.42 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.165 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.222 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28397 597 4.7 %RANDOM
Rwork0.20651 ---
obs0.21009 11983 99.72 %-
all-12580 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.889 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20.41 Å20 Å2
2--0.82 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 2.25→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1226 0 43 136 1405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0390.0211285
X-RAY DIFFRACTIONr_angle_refined_deg3.0342.0231743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8495164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22920.19651
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.05615210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3381521
X-RAY DIFFRACTIONr_chiral_restr0.1890.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02950
X-RAY DIFFRACTIONr_nbd_refined0.2230.2284
X-RAY DIFFRACTIONr_nbtor_refined0.2770.2689
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3770.265
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.22
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5260.27
X-RAY DIFFRACTIONr_mcbond_it2.3511.5952
X-RAY DIFFRACTIONr_mcangle_it2.34821288
X-RAY DIFFRACTIONr_scbond_it4.0413507
X-RAY DIFFRACTIONr_scangle_it5.8284.5455
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 27 -
Rwork0.25 881 -
obs--100 %

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