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- PDB-8x5s: Crystal structure of shikimate kinase of Mycobacterium tuberculos... -

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Basic information

Entry
Database: PDB / ID: 8x5s
TitleCrystal structure of shikimate kinase of Mycobacterium tuberculosis complex with shikimate-3-phosphate
ComponentsShikimate kinase
KeywordsTRANSFERASE / Shikimate Kinase / Mycobacterium tuberculosis / shikimate-3-phosphate
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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
SHIKIMATE-3-PHOSPHATE / Shikimate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.726 Å
AuthorsYadav, A.K. / Madhuri, M. / Saini, C. / Inampudi, K.K. / Ethayathulla, A.S. / Kumar, M.
Funding support India, 1items
OrganizationGrant numberCountry
Indian Council of Medical Research India
CitationJournal: To Be Published
Title: Crystal structure of shikimate kinase of Mycobacterium tuberculosis complex with shikimate-3-phosphate
Authors: Yadav, A.K. / Kumar, M. / Ethayathulla, A.S. / Madhuri, M. / Saini, C.
History
DepositionNov 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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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)19,2516
Polymers18,6121
Non-polymers6385
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.424, 59.424, 102.250
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-352-

HOH

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Components

#1: Protein Shikimate kinase


Mass: 18612.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: aroK / Production host: Escherichia coli (E. coli) / References: UniProt: P9WPY3, shikimate kinase
#2: Chemical ChemComp-S3P / SHIKIMATE-3-PHOSPHATE


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


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulphate 0.1 M Sodium acetate trihydrate pH - 4.6 30% PEG 2000

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.72→46.011 Å / Num. obs: 21710 / % possible obs: 96 % / Redundancy: 9.1 % / Biso Wilson estimate: 29.5 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.022 / Rrim(I) all: 0.067 / Net I/σ(I): 18.8
Reflection shellResolution: 1.72→1.756 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.072 / Num. unique obs: 1122 / CC1/2: 0.913 / Rpim(I) all: 0.369 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IYX

2iyx


Resolution: 1.726→46.011 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.172 / SU B: 2.587 / SU ML: 0.08 / Average fsc free: 0.9576 / Average fsc work: 0.9694 / Cross valid method: FREE R-VALUE / ESU R: 0.1 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2222 1144 5.271 %
Rwork0.1761 20560 -
all0.179 --
obs-21704 95.98 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.003 Å2-0.002 Å2-0 Å2
2---0.003 Å20 Å2
3---0.011 Å2
Refinement stepCycle: LAST / Resolution: 1.726→46.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1252 0 36 146 1434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121348
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161354
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.8471837
X-RAY DIFFRACTIONr_angle_other_deg0.5941.7713090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4825179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.865525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0310227
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.4071054
X-RAY DIFFRACTIONr_chiral_restr0.0870.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021654
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02322
X-RAY DIFFRACTIONr_nbd_refined0.2460.2311
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.21191
X-RAY DIFFRACTIONr_nbtor_refined0.1950.2637
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2713
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2102
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1090.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3470.222
X-RAY DIFFRACTIONr_nbd_other0.2110.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1750.219
X-RAY DIFFRACTIONr_mcbond_it3.143.176691
X-RAY DIFFRACTIONr_mcbond_other3.1123.174691
X-RAY DIFFRACTIONr_mcangle_it4.4565.682867
X-RAY DIFFRACTIONr_mcangle_other4.4585.685868
X-RAY DIFFRACTIONr_scbond_it4.8843.897657
X-RAY DIFFRACTIONr_scbond_other4.6243.85636
X-RAY DIFFRACTIONr_scangle_it7.246.852965
X-RAY DIFFRACTIONr_scangle_other7.0856.772942
X-RAY DIFFRACTIONr_lrange_it11.30539.5351543
X-RAY DIFFRACTIONr_lrange_other11.26235.7181511
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.726-1.7710.333800.30915560.3116420.9060.91999.63460.254
1.771-1.8190.322820.27515180.27716040.9170.93899.75060.221
1.819-1.8720.271020.25414520.25515560.9470.9599.87150.195
1.872-1.9290.249690.2314370.23115060.9610.9631000.184
1.929-1.9930.317700.2114120.21414820.9330.9691000.168
1.993-2.0620.2710.19112430.19114230.9730.97692.34010.157
2.062-2.140.227470.1739360.17613720.9680.9871.64720.148
2.14-2.2270.22710.16112430.16413140.970.9831000.138
2.227-2.3260.194660.1648180.16612760.980.98369.2790.142
2.326-2.4390.203700.16711450.16912150.9750.9831000.148
2.439-2.5710.274560.16711300.17211860.9550.9831000.148
2.571-2.7260.229570.1610380.16310950.9630.9831000.146
2.726-2.9140.208740.1649600.16710340.9710.9821000.155
2.914-3.1460.215460.1669430.1699890.9720.9831000.162
3.146-3.4450.205410.1588650.169060.9730.9851000.162
3.445-3.8490.174400.1617710.1628110.9820.9861000.175
3.849-4.4390.178340.1387010.1397350.9820.9881000.158
4.439-5.4240.249270.1536180.1586450.9780.9861000.178
5.424-7.6180.241270.2214720.2224990.9670.971000.247
7.618-46.0110.237140.2283020.2293160.9460.9691000.288

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