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- PDB-4bqs: Crystal structure of Mycobacterium tuberculosis shikimate kinase ... -

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Basic information

Entry
Database: PDB / ID: 4bqs
TitleCrystal structure of Mycobacterium tuberculosis shikimate kinase in complex with ADP and a shikimic acid derivative.
ComponentsSHIKIMATE KINASE
KeywordsTRANSFERASE / PHOSPHOTRANSFERASES (ALCOHOL GROUP ACCEPTOR) / SHIKIMIC ACID PATHWAY / INHIBITOR
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 / Chem-K2Q / Shikimate kinase / Shikimate kinase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsOtero, J.M. / Garcia-Doval, C. / Llamas-Saiz, A.L. / Blanco, B. / Prado, V. / Lence, E. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C. / van Raaij, M.J.
CitationJournal: J. Am. Chem. Soc. / Year: 2013
Title: Mycobacterium tuberculosis shikimate kinase inhibitors: design and simulation studies of the catalytic turnover.
Authors: Blanco, B. / Prado, V. / Lence, E. / Otero, J.M. / Garcia-Doval, C. / van Raaij, M.J. / Llamas-Saiz, A.L. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C.
History
DepositionJun 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Feb 7, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.4Dec 20, 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
C: SHIKIMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7559
Polymers55,8373
Non-polymers1,9186
Water2,540141
1
A: SHIKIMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2523
Polymers18,6121
Non-polymers6392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SHIKIMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2523
Polymers18,6121
Non-polymers6392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SHIKIMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2523
Polymers18,6121
Non-polymers6392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.653, 60.959, 89.976
Angle α, β, γ (deg.)90.00, 95.44, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.13579, 0.76259, -0.63247), (-0.76588, -0.48576, -0.42126), (-0.62848, 0.4272, 0.65001)50.78946, 24.22085, -10.92785
2given(0.17682, -0.75102, 0.63617), (-0.74685, -0.52336, -0.41025), (0.64105, -0.40258, -0.65344)-20.30539, 55.58348, 99.54014
3given(0.14478, 0.75556, 0.63888), (0.77184, -0.49025, 0.40487), (0.61911, 0.43449, -0.65415)-83.81224, -22.23803, 103.53188

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Components

#1: Protein SHIKIMATE KINASE / SK


Mass: 18612.352 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A4Z2, UniProt: P9WPY3*PLUS, shikimate kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-K2Q / (1R,6R,10S)-6,10-dihydroxy-2-oxabicyclo[4.3.1]deca-4(Z),7-diene-8-carboxylic acid


Mass: 212.199 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H12O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.07 Å3/Da / Density % sol: 40.63 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: VAPOR DIFUSION, SITTING DROP, 20% (W/V) PEG 3350, 500 MM LICL AND 100 MM TRIS.HCL PH 7.8, ATP, SHIKIMIC ACID DERIVATIVE, TEMPERATURE 291 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9798
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: May 3, 2013 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.15→28.85 Å / Num. obs: 22876 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.1
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.5 / % possible all: 79.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G1K

2g1k


Resolution: 2.15→28.87 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.399 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.327 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY RESIDUES 171-176 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.23506 1165 5.1 %RANDOM
Rwork0.1723 ---
obs0.17554 21698 95.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.371 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å22.91 Å2
2---0.79 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.15→28.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3774 0 126 141 4041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193954
X-RAY DIFFRACTIONr_bond_other_d0.0020.023945
X-RAY DIFFRACTIONr_angle_refined_deg1.7472.0215370
X-RAY DIFFRACTIONr_angle_other_deg0.8563.0038988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8535504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.21320.385156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56215645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3781563
X-RAY DIFFRACTIONr_chiral_restr0.0850.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214419
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02897
X-RAY DIFFRACTIONr_nbd_refined0.2390.2986
X-RAY DIFFRACTIONr_nbd_other0.1690.23817
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21974
X-RAY DIFFRACTIONr_nbtor_other0.0840.22592
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1450.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3470.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1630.2107
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.28
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0180.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4673.0253954
X-RAY DIFFRACTIONr_mcbond_other0.5793.0843945
X-RAY DIFFRACTIONr_mcangle_it3.7774.4835370
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.81229.0662955
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.9539.535456
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: 2.15→2.266 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.316 138 -
Rwork0.231 2625 -
obs--79.03 %

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