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- PDB-1l4y: CRYSTAL STRUCTURE OF SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCUL... -

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Basic information

Entry
Database: PDB / ID: 1l4y
TitleCRYSTAL STRUCTURE OF SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MGADP AT 2.0 ANGSTROM RESOLUTION
ComponentsSHIKIMATE KINASE
KeywordsTRANSFERASE / SHIKIMATE PATHWAY / SHIKIMATE KINASE / PHORSPHORYL TRANSFER / DRUG DESIGN
Function / homology
Function and homology information


shikimate kinase / shikimate metabolic process / shikimate kinase activity / Chorismate via Shikimate Pathway / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / phosphorylation / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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 / Difference Fourier / Resolution: 2 Å
AuthorsGu, Y. / Reshetnikova, L. / Li, Y. / Wu, Y. / Yan, H. / Singh, S. / Ji, X.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of shikimate kinase from Mycobacterium tuberculosis reveals the dynamic role of the LID domain in catalysis.
Authors: Gu, Y. / Reshetnikova, L. / Li, Y. / Wu, Y. / Yan, H. / Singh, S. / Ji, X.
History
DepositionMar 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 29, 2017Group: Refinement description
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID

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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)19,2418
Polymers18,6121
Non-polymers6297
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.86, 63.86, 92.07
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-195-

CL

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Components

#1: Protein SHIKIMATE KINASE / / SK


Mass: 18612.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: AROK / Plasmid: PET-17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A4Z2, UniProt: P9WPY3*PLUS, shikimate kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.91 Å3/Da / Density % sol: 57.74 %
Crystal growTemperature: 288.2 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, Magnesium Choloride, Sodium Chloride, ADENOSINE-5'-DIPHOSPHATE, SHIKIMIC ACID, Na-HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.2K
Crystal grow
*PLUS
Details: Gu, Y., (2001) Acta Crystallogr, D57, 1870.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMsodium HEPES1droppH7.5
20.5 M1dropNaCl
35.0 mM1dropMgCl2
45.0 mMsgikimate acid1drop
55.0 mMADP1drop
67.0 mg/mlprotein1drop
720 %PEG40001reservoir
810 %2-propanol1reservoir
90.1 Msodium HEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 1999 / Details: MIRROR
RadiationMonochromator: Silicon (111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2→27.65 Å / Num. all: 15110 / Num. obs: 14820 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.88 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.056 / Net I/σ(I): 26.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 4.64 / Num. unique all: 1461 / Rsym value: 0.41 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / % possible obs: 99.5 % / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.63

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: Difference Fourier
Starting model: PDB ENTRY 1L4U

1l4u


Resolution: 2→30 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 251349.94 / Data cutoff high rms absF: 251349.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 739 5 %RANDOM
Rwork0.217 ---
all-14820 --
obs-14820 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.129 Å2 / ksol: 0.376723 e/Å3
Displacement parametersBiso mean: 35.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.76 Å2-0.78 Å20 Å2
2--3.76 Å20 Å2
3----7.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-30 Å
Luzzati sigma a0.27 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1226 0 33 173 1432
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.991.5
X-RAY DIFFRACTIONc_mcangle_it2.872
X-RAY DIFFRACTIONc_scbond_it3.012
X-RAY DIFFRACTIONc_scangle_it4.312.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 121 5.1 %
Rwork0.274 2242 -
obs-1592 96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4PARAM.ADPTOPOL.ADP
X-RAY DIFFRACTION5PARAM.HEPTOPOL.HEP
Refinement
*PLUS
Highest resolution: 2.03 Å / Lowest resolution: 30 Å / Rfactor obs: 0.217 / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Rfactor Rfree: 0.298 / Rfactor Rwork: 0.274 / Rfactor obs: 0.274

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