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

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Basic information

Entry
Database: PDB / ID: 2iyu
TitleShikimate kinase from Mycobacterium tuberculosis in complex with ADP, 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
ADENOSINE-5'-DIPHOSPHATE / Shikimate kinase / Shikimate kinase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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

Downloads & links

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Assembly

Deposited unit
A: SHIKIMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1463
Polymers19,6841
Non-polymers4632
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.306, 44.306, 150.076
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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 162 / 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: 30.3 %
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: Sep 24, 2005 / Details: MORRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.85→19.81 Å / Num. obs: 13255 / % possible obs: 98 % / Redundancy: 4.67 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.38
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.05 / % possible all: 99.5

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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: 1.85→19.81 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.859 / SU B: 4.544 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.295 680 5.1 %RANDOM
Rwork0.214 ---
obs0.218 12575 98 %-
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: 26.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1241 0 28 162 1431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221335
X-RAY DIFFRACTIONr_bond_other_d0.0020.021312
X-RAY DIFFRACTIONr_angle_refined_deg1.8492.0071820
X-RAY DIFFRACTIONr_angle_other_deg0.91533008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7035180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96520.52657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41615227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1841523
X-RAY DIFFRACTIONr_chiral_restr0.10.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021506
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02292
X-RAY DIFFRACTIONr_nbd_refined0.2180.2320
X-RAY DIFFRACTIONr_nbd_other0.210.21367
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2629
X-RAY DIFFRACTIONr_nbtor_other0.0880.2830
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2110
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.12121083
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.732161352
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it12.44324536
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it14.45136461
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: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.381 52
Rwork0.229 898

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