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- PDB-3tr1: Structure of a 3-phosphoshikimate 1-carboxyvinyltransferase (aroA... -

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Basic information

Entry
Database: PDB / ID: 3tr1
TitleStructure of a 3-phosphoshikimate 1-carboxyvinyltransferase (aroA) from Coxiella burnetii
Components3-phosphoshikimate 1-carboxyvinyltransferase
KeywordsTRANSFERASE / Amino acid biosynthesis
Function / homology
Function and homology information


3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytoplasm
Similarity search - Function
EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / EPSP synthase signature 2. / Enolpyruvate transferase domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) ...EPSP synthase signature 1. / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase, conserved site / EPSP synthase signature 2. / Enolpyruvate transferase domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / 3-phosphoshikimate 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsCheung, J. / Franklin, M.C. / 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 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Feb 10, 2016Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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

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Assembly

Deposited unit
A: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9547
Polymers47,4401
Non-polymers5146
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.026, 94.026, 233.086
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein 3-phosphoshikimate 1-carboxyvinyltransferase / 5-enolpyruvylshikimate-3-phosphate synthase / EPSP synthase / EPSPS


Mass: 47440.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: aroA, CBU_0526 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q83E11, 3-phosphoshikimate 1-carboxyvinyltransferase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.13 Å3/Da / Density % sol: 60.76 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.1M glycine pH 10.5, 0.2M lithium sulfate, 1.2M sodium hydrogen phosphate, 0.8M potassium dihydrogen phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: Mar 3, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 4.6 % / Av σ(I) over netI: 21.96 / Number: 351355 / Rmerge(I) obs: 0.083 / Χ2: 1.44 / D res high: 2 Å / D res low: 30 Å / Num. obs: 76948 / % possible obs: 98.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.423091.810.0523.2844.6
4.315.4296.910.0633.7574.7
3.764.3195.910.0663.5124.7
3.423.7696.810.0733.0714.7
3.173.4297.810.0822.5764.8
2.993.1798.210.0932.0444.8
2.842.9998.910.1031.6614.7
2.712.8499.610.1141.3014.7
2.612.7199.710.1281.0634.7
2.522.6199.410.1350.9354.7
2.442.5299.510.1580.7884.7
2.372.4499.610.1680.7064.7
2.312.3799.610.1950.6084.6
2.252.3199.610.2260.5514.6
2.22.2599.510.2420.4854.6
2.152.299.710.3120.4334.6
2.112.1599.810.3340.3994.6
2.072.1199.310.3920.3684.4
2.032.0797.910.4270.364
22.0395.710.4810.3443.4
ReflectionResolution: 2→30 Å / Num. all: 78278 / Num. obs: 76948 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.083 / Χ2: 1.439 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.033.40.48137410.344195.7
2.03-2.0740.42737990.36197.9
2.07-2.114.40.39239000.368199.3
2.11-2.154.60.33439150.399199.8
2.15-2.24.60.31239140.433199.7
2.2-2.254.60.24238690.485199.5
2.25-2.314.60.22639220.551199.6
2.31-2.374.60.19539000.608199.6
2.37-2.444.70.16838670.706199.6
2.44-2.524.70.15839110.788199.5
2.52-2.614.70.13538980.935199.4
2.61-2.714.70.12838901.063199.7
2.71-2.844.70.11439011.301199.6
2.84-2.994.70.10338621.661198.9
2.99-3.174.80.09338502.044198.2
3.17-3.424.80.08238332.576197.8
3.42-3.764.70.07337943.071196.8
3.76-4.314.70.06637673.512195.9
4.31-5.424.70.06337913.757196.9
5.42-304.60.05236243.284191.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→29.947 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8847 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.83 / Stereochemistry target values: ML / Details: THE FRIEDEL PAIRS WERE USED FOR phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.1949 2124 5.07 %RANDOM
Rwork0.1784 ---
obs0.1793 41927 99.11 %-
all-44446 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.853 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso max: 287.78 Å2 / Biso mean: 43.7512 Å2 / Biso min: 20.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.7355 Å20 Å2-0 Å2
2--0.7355 Å2-0 Å2
3----1.471 Å2
Refinement stepCycle: LAST / Resolution: 2→29.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3234 0 26 276 3536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073302
X-RAY DIFFRACTIONf_angle_d1.074475
X-RAY DIFFRACTIONf_chiral_restr0.073530
X-RAY DIFFRACTIONf_plane_restr0.004582
X-RAY DIFFRACTIONf_dihedral_angle_d12.1381230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.06750.29522060.23913835404198
2.0675-2.15020.19082120.195139154127100
2.1502-2.2480.24482040.188239384142100
2.248-2.36650.22142060.190539644170100
2.3665-2.51470.20261950.187339644159100
2.5147-2.70880.20882270.191839684195100
2.7088-2.98110.21592230.186639674190100
2.9811-3.4120.20952360.18773996423299
3.412-4.29670.1772040.16084074427899
4.2967-29.950.16212110.16694182439396
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)
11.69850.32490.70520.7242-0.11240.44050.0629-0.1216-0.15240.0271-0.0470.1407-0.0463-0.196-0.02330.14670.0205-0.01240.33990.02490.230242.606646.60991.6604
21.88030.20511.21661.1730.34850.94330.196-0.91210.03570.2782-0.1362-0.12650.0524-0.3342-0.03330.2494-0.05850.010.70610.05940.232539.126942.55121.1758
34.1663-0.335-4.08850.714-0.00324.39440.0855-10.09390.5068-0.06360.3178-0.20850.0938-0.02420.35030.05860.02640.7404-0.1160.322135.446554.692822.5301
40.10830.1599-0.2351.04760.96212.56310.094-0.4420.36410.0028-0.16960.2452-0.4862-0.28320.13140.30020.08620.02780.5951-0.10950.432934.868561.328412.642
50.9838-0.1982-0.02520.4158-0.27761.35110.01750.06420.35790.0333-0.07780.052-0.50190.0030.05590.3192-0.0014-0.01120.31560.04570.409156.647364.16961.7051
60.6763-0.0875-0.9040.51840.21472.140.1182-0.09990.4495-0.12340.0278-0.2496-0.2510.5885-0.12550.3387-0.1007-0.00550.38090.05540.471271.441866.68595.0829
70.38580.062-0.05921.01530.37411.1270.0172-0.0192-0.06840.0759-0.0735-0.0545-0.04920.08310.05610.1673-0.0407-0.03210.35030.02280.257766.429452.123613.3272
80.55020.1078-0.70870.7769-0.13071.0320.09230.4674-0.33660.0806-0.0925-0.01980.0024-0.3111-0.0260.1422-0.0225-0.0340.3820.00720.287261.253144.6413-2.4117
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 0:94)A0 - 94
2X-RAY DIFFRACTION2(chain A and resid 95:154)A95 - 154
3X-RAY DIFFRACTION3(chain A and resid 155:182)A155 - 182
4X-RAY DIFFRACTION4(chain A and resid 183:232)A183 - 232
5X-RAY DIFFRACTION5(chain A and resid 233:295)A233 - 295
6X-RAY DIFFRACTION6(chain A and resid 296:303)A296 - 303
7X-RAY DIFFRACTION7(chain A and resid 304:408)A304 - 408
8X-RAY DIFFRACTION8(chain A and resid 409:436)A409 - 436

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