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- PDB-2iyr: Shikimate kinase from Mycobacterium tuberculosis in complex with ... -

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Basic information

Entry
Database: PDB / ID: 2iyr
TitleShikimate kinase from Mycobacterium tuberculosis in complex with shikimate
ComponentsSHIKIMATE KINASE
KeywordsTRANSFERASE / AROMATIC AMINO ACID BIOSYNTHESIS / KINASE / MAGNESIUM / P-LOOP KINASE / METAL-BINDING / SHIKIMATE KINASE / SHIKIMATE PATHWAY / NUCLEOTIDE-BINDING / AMINO-ACID BIOSYNTHESIS / 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
Chem-SKM / Shikimate kinase / Shikimate kinase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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 21, 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

Downloads & links

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Assembly

Deposited unit
A: SHIKIMATE KINASE
B: SHIKIMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7154
Polymers39,3672
Non-polymers3482
Water4,071226
1
A: SHIKIMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8582
Polymers19,6841
Non-polymers1741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SHIKIMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8582
Polymers19,6841
Non-polymers1741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.444, 41.836, 44.408
Angle α, β, γ (deg.)90.00, 113.99, 90.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein SHIKIMATE KINASE / SK


Mass: 19683.506 Da / Num. of mol.: 2
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-SKM / (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID / SHIKIMATE


Mass: 174.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 32 %
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: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 17, 2006 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.98→19.54 Å / Num. obs: 19559 / % possible obs: 96.1 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.97
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 2 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.48 / % possible all: 92.9

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Processing

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

2iyq


Resolution: 1.98→41.85 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.218 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 986 5 %RANDOM
Rwork0.165 ---
obs0.169 18573 96.1 %-
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: 27.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å2-0.03 Å20.63 Å2
2--0.87 Å2-0.78 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.98→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2457 0 24 226 2707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222536
X-RAY DIFFRACTIONr_bond_other_d0.0020.022509
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.993431
X-RAY DIFFRACTIONr_angle_other_deg0.88535745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8425335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.32120.385104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10415428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8731542
X-RAY DIFFRACTIONr_chiral_restr0.090.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022859
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02545
X-RAY DIFFRACTIONr_nbd_refined0.2250.2549
X-RAY DIFFRACTIONr_nbd_other0.2010.22541
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21218
X-RAY DIFFRACTIONr_nbtor_other0.0870.21507
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2171
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2930.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.74562112
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.24682613
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.88312965
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it11.43218814
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: 1.98→2.03 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.337 79
Rwork0.229 1337

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