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- PDB-3trf: Structure of a shikimate kinase (aroK) from Coxiella burnetii -

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Basic information

Entry
Database: PDB / ID: 3trf
TitleStructure of a shikimate kinase (aroK) from Coxiella burnetii
ComponentsShikimate kinase
KeywordsTRANSFERASE / Amino acid biosynthesis
Function / homology
Function and homology information


shikimate kinase / shikimate metabolic process / shikimate kinase activity / chorismate biosynthetic process / aromatic amino acid family 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsCheung, J. / Franklin, M. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 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_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5074
Polymers42,3152
Non-polymers1922
Water1,51384
1
A: Shikimate kinase
hetero molecules

A: Shikimate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5074
Polymers42,3152
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area4540 Å2
ΔGint-58 kcal/mol
Surface area15820 Å2
MethodPISA
2
B: Shikimate kinase
hetero molecules

B: Shikimate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5074
Polymers42,3152
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area4670 Å2
ΔGint-60 kcal/mol
Surface area15320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.429, 98.429, 157.071
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-62-

ARG

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Components

#1: Protein Shikimate kinase / / SK


Mass: 21157.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: aroK, CBU_1892 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83AJ3, shikimate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG3350, 0.2 M potassium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 28, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 20758 / Num. obs: 20447 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.3-2.348.50.39192.6
2.34-2.389.90.368194.4
2.38-2.4310.70.318198.3
2.43-2.4812.20.323199.9
2.48-2.5313.40.2641100
2.53-2.5913.80.2111100
2.59-2.6614.30.2111100
2.66-2.7314.40.1761100
2.73-2.8114.20.151100
2.81-2.914.20.1231100
2.9-314.40.1151100
3-3.1214.20.0931100
3.12-3.2614.20.0751100
3.26-3.4414.20.0651100
3.44-3.65140.0581100
3.65-3.93140.051199.9
3.93-4.3313.90.048199.8
4.33-4.9513.50.045199.6
4.95-6.2413.40.045199.6
6.24-5011.50.042187.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KAG

1kag


Resolution: 2.6→41.703 Å / Occupancy max: 1 / Occupancy min: 0.8 / SU ML: 0.41 / σ(F): 0 / Phase error: 27.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2702 728 5.09 %
Rwork0.2055 --
obs0.2087 14293 98.89 %
all-15189 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.6 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.447 Å20 Å20 Å2
2---6.447 Å20 Å2
3---12.894 Å2
Refinement stepCycle: LAST / Resolution: 2.6→41.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 0 10 84 2775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032727
X-RAY DIFFRACTIONf_angle_d0.7023662
X-RAY DIFFRACTIONf_dihedral_angle_d13.9151078
X-RAY DIFFRACTIONf_chiral_restr0.05420
X-RAY DIFFRACTIONf_plane_restr0.002470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80070.35931590.28012646X-RAY DIFFRACTION100
2.8007-3.08250.34831470.26262673X-RAY DIFFRACTION100
3.0825-3.52840.29341620.20552681X-RAY DIFFRACTION100
3.5284-4.44460.24361260.18262766X-RAY DIFFRACTION100
4.4446-41.70810.22481340.19092799X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.13520.01370.06020.3055-0.15970.1238-0.1688-0.1402-0.16480.1361-0.01080.2633-0.16620.0105-0.00070.39820.10760.15890.33940.10280.459331.272925.6721-1.8384
20.03920.01520.03470.02450.03090.3336-0.1519-0.0023-0.0180.1333-0.17450.1871-0.0206-0.05890.17960.44330.08170.01710.37440.02210.723729.863723.4373-14.6665
30.2249-0.2220.07280.51060.01850.1119-0.03660.1161-0.121-0.01220.03420.4177-0.0313-0.0675-0.16220.36460.1571-0.13580.2206-0.00130.448330.922633.4116-20.6843
40.192-0.03190.1010.0099-0.01820.33-0.166-0.08540.02840.0193-0.02950.3073-0.1045-0.1871-0.15040.33150.20590.20150.27690.01150.678626.069134.3163-6.3267
50.2744-0.10940.02240.3992-0.02550.0041-0.0462-0.1430.1057-0.0154-0.1032-0.1419-0.07620.01780.02250.28620.1053-0.0610.26390.08130.268851.013726.243-6.6183
60.4617-0.26170.1050.1509-0.01480.7843-0.3413-0.32920.07450.31590.1211-0.115-0.18940.2207-0.04570.52010.165-0.01060.2579-0.02150.295937.261533.75491.4253
70.13950.009-0.09410.06450.03350.0956-0.1433-0.05820.06770.1434-0.1092-0.1567-0.03120.0973-0.17320.44030.127-0.16770.3082-0.03310.256729.727367.673-1.7852
80.2695-0.1304-0.31150.36810.41520.6285-0.04430.0714-0.06030.114-0.0921-0.1002-0.0879-0.10960.03630.46690.15950.09190.39650.00610.30829.47567.0183-17.1354
90.2369-0.0015-0.10480.280.07360.5089-0.18160.2229-0.1638-0.1725-0.1885-0.29980.0817-0.0942-0.72380.21350.37890.09860.07-0.3050.310331.29659.9524-17.3273
100.2139-0.0958-0.00280.3939-0.10840.209-0.1377-0.107-0.1460.37540.0391-0.11460.1084-0.0782-0.10870.38430.13860.00280.20490.03840.266927.104656.9195-4.7589
110.3601-0.1690.01040.1579-0.14780.25940.0835-0.0374-0.2067-0.2103-0.09260.18760.13170.03740.02680.51210.07210.08410.2877-0.08950.43767.171769.0566-9.8609
120.0113-0.0462-0.02450.38210.06790.0714-0.1416-0.0306-0.09020.1445-0.06450.28980.1154-0.0767-0.2110.57240.14450.29270.14410.1170.668718.063550.517-5.538
13-0.00010.0053-0.00130.07970.0022-0.0003-0.0149-0.13210.10.21540.07940.0285-0.2313-0.2841-0.0010.97590.2501-0.15370.56640.01660.255727.269165.34817.752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:29)
2X-RAY DIFFRACTION2chain 'A' and (resseq 30:47)
3X-RAY DIFFRACTION3chain 'A' and (resseq 48:73)
4X-RAY DIFFRACTION4chain 'A' and (resseq 74:105)
5X-RAY DIFFRACTION5chain 'A' and (resseq 106:128)
6X-RAY DIFFRACTION6chain 'A' and (resseq 129:174)
7X-RAY DIFFRACTION7chain 'B' and (resseq 6:32)
8X-RAY DIFFRACTION8chain 'B' and (resseq 33:47)
9X-RAY DIFFRACTION9chain 'B' and (resseq 48:82)
10X-RAY DIFFRACTION10chain 'B' and (resseq 83:116)
11X-RAY DIFFRACTION11chain 'B' and (resseq 117:128)
12X-RAY DIFFRACTION12chain 'B' and (resseq 129:149)
13X-RAY DIFFRACTION13chain 'B' and (resseq 150:173)

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