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- PDB-2iyt: Shikimate kinase from Mycobacterium tuberculosis in unliganded st... -

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Basic information

Entry
Database: PDB / ID: 2iyt
TitleShikimate kinase from Mycobacterium tuberculosis in unliganded state, open LID (conf. A)
ComponentsSHIKIMATE KINASE
KeywordsTRANSFERASE / AROMATIC AMINO ACID BIOSYNTHESIS / P-LOOP KINASE / METAL- BINDING / SHIKIMATE KINASE / SHIKIMATE PATHWAY / NUCLEOTIDE- BINDING / AMINO-ACID BIOSYNTHESIS / KINASE / MAGNESIUM / ATP-BINDING
Function / homology
Function and homology information


shikimate kinase / shikimate kinase activity / shikimate metabolic process / Chorismate via Shikimate Pathway / 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
Shikimate kinase / Shikimate kinase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsHartmann, M.D. / Bourenkov, G.P. / Oberschall, A. / Strizhov, N. / Bartunik, H.D.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Mechanism of Phosphoryl Transfer Catalyzed by Shikimate Kinase from Mycobacterium Tuberculosis.
Authors: Hartmann, M.D. / Bourenkov, G.P. / Oberschall, A. / Strizhov, N. / Bartunik, H.D.
History
DepositionJul 22, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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)19,7192
Polymers19,6841
Non-polymers351
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.192, 44.192, 152.628
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein SHIKIMATE KINASE / SK


Mass: 19683.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P0A4Z2, UniProt: P9WPY3*PLUS, shikimate kinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC-TERMINAL HIS-TAG

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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: 1.8 Å3/Da / Density % sol: 31.1 %
Crystal growpH: 8.5
Details: 170MM NA ACETATE, 15%(V/V) GLYCEROL, 25.5%(W/V) PEG 4000, 85MM TRIS-HCL PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9786
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 7, 2005 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.47→19.73 Å / Num. obs: 26142 / % possible obs: 97.6 % / Redundancy: 4.05 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.15
Reflection shellResolution: 1.47→1.51 Å / Redundancy: 4 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.04 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IYS

2iys


Resolution: 1.47→19.73 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1298 5 %RANDOM
Rwork0.197 ---
obs0.199 24844 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.47→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1293 0 1 192 1486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221450
X-RAY DIFFRACTIONr_bond_other_d00.021464
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.9951997
X-RAY DIFFRACTIONr_angle_other_deg3.57133388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1655215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55320.50859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95915264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5851524
X-RAY DIFFRACTIONr_chiral_restr0.1170.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021672
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02312
X-RAY DIFFRACTIONr_nbd_refined0.2280.2277
X-RAY DIFFRACTIONr_nbd_other0.2330.21313
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2694
X-RAY DIFFRACTIONr_nbtor_other0.1020.2818
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2107
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3320.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.9918933
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.532241519
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it14.1536517
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it16.11354455
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.47→1.51 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.474 103
Rwork0.364 1775

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