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

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Basic information

Entry
Database: PDB / ID: 2iyy
TitleShikimate kinase from Mycobacterium tuberculosis in complex with shikimate-3-phosphate and SO4
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
PHOSPHATE ION / SHIKIMATE-3-PHOSPHATE / Shikimate kinase / Shikimate kinase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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 / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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)20,84915
Polymers19,6841
Non-polymers1,16514
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.349, 59.349, 102.867
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-205-

SO4

21A-213-

MG

31A-2172-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 6 types, 256 molecules

#2: Chemical ChemComp-S3P / SHIKIMATE-3-PHOSPHATE


Mass: 254.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11O8P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growpH: 8 / Details: 200MM MGSO4, 20%(W/V) PEG 3350, pH 8.00

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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: Aug 10, 2005 / 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: 1.62→19.16 Å / Num. obs: 25604 / % possible obs: 93.8 % / Redundancy: 2.31 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 5.7
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.4 / % possible all: 92.5

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Processing

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

2iyx


Resolution: 1.62→19.16 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.33 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1321 5.2 %RANDOM
Rwork0.175 ---
obs0.178 24283 93.8 %-
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: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20.7 Å20 Å2
2--1.41 Å20 Å2
3----2.11 Å2
Refinement stepCycle: LAST / Resolution: 1.62→19.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1258 0 61 242 1561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221635
X-RAY DIFFRACTIONr_bond_other_d0.0060.021619
X-RAY DIFFRACTIONr_angle_refined_deg1.6512.0222230
X-RAY DIFFRACTIONr_angle_other_deg0.90533727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6975205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.03819.85368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15315296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1391530
X-RAY DIFFRACTIONr_chiral_restr0.1020.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021772
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02348
X-RAY DIFFRACTIONr_nbd_refined0.2190.2307
X-RAY DIFFRACTIONr_nbd_other0.2120.21581
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2645
X-RAY DIFFRACTIONr_nbtor_other0.0850.2891
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2171
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.022121288
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.137161627
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it10.35924674
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it13.47436600
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: 1.62→1.66 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.334 94
Rwork0.268 1726

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