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- PDB-3roi: 2.20 Angstrom resolution structure of 3-phosphoshikimate 1-carbox... -

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Basic information

Entry
Database: PDB / ID: 3roi
Title2.20 Angstrom resolution structure of 3-phosphoshikimate 1-carboxyvinyltransferase (AroA) from Coxiella burnetii
Components3-phosphoshikimate 1-carboxyvinyltransferase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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
3-phosphoshikimate 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLight, S.H. / Minasov, G. / Krishna, S.N. / Halavaty, A.S. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 2.20 Angstrom resolution structure of 3-phosphoshikimate 1-carboxyvinyltransferase (AroA) from Coxiella burnetii
Authors: Light, S.H. / Minasov, G. / Krishna, S.N. / Halavaty, A.S. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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 / 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: 3-phosphoshikimate 1-carboxyvinyltransferase
B: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,18622
Polymers93,5072
Non-polymers1,67920
Water3,567198
1
A: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,84613
Polymers46,7541
Non-polymers1,09212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3409
Polymers46,7541
Non-polymers5878
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-269 kcal/mol
Surface area33940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.164, 116.408, 160.749
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 46753.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA 493 / Gene: aroA, CBU_0526 / Plasmid: MCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q83E11, 3-phosphoshikimate 1-carboxyvinyltransferase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 7.5 mg/ml, 0.5 M NaCl, 0.01 Tris, JCSG+, B1 0.8 M Ammonium Sulfate, 0.1 M tri-Sodium Citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 17, 2011 / Details: Beryllium lens
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 40980 / Num. obs: 40980 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 49.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 51

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
BALBESphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RF5

1rf5


Resolution: 2.2→29.1 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 13.469 / SU ML: 0.159 / Isotropic thermal model: Individual thermal factors refined / Cross valid method: THROUGHOUT / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24308 2034 5 %RANDOM
Rwork0.19054 ---
all0.19323 38869 --
obs0.19323 38869 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.292 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2--0.67 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6400 0 84 198 6682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226647
X-RAY DIFFRACTIONr_bond_other_d0.0010.024430
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.9989039
X-RAY DIFFRACTIONr_angle_other_deg0.846310913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7285878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.27424.458249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.97151139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1661545
X-RAY DIFFRACTIONr_chiral_restr0.0840.21065
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217372
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021185
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9521.54332
X-RAY DIFFRACTIONr_mcbond_other0.2531.51778
X-RAY DIFFRACTIONr_mcangle_it1.74326991
X-RAY DIFFRACTIONr_scbond_it2.87232315
X-RAY DIFFRACTIONr_scangle_it4.6384.52047
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 126 -
Rwork0.215 2660 -
obs-2660 94.57 %
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)
12.3428-2.0444-0.75333.10520.88820.93480.0575-0.15780.1618-0.1330.1004-0.104-0.10650.1281-0.15780.0251-0.01320.0290.023-0.02820.0748-4.245927.8821-32.919
22.2928-0.1165-0.12322.1261-0.03232.3429-0.0431-0.2637-0.2611-0.05220.11080.64810.1613-0.1766-0.06770.12780.03960.04210.17080.0350.3064-23.211128.9947-28.6566
31.1419-1.7607-0.02734.01490.49890.3178-0.1291-0.3583-0.14390.39960.23930.12760.1635-0.0055-0.11020.19280.0430.0240.2490.01210.1204-3.843617.213-23.0921
41.37710.5515-0.53581.5716-0.03971.94560.0954-0.1957-0.01390.2206-0.0390.01390.1347-0.0508-0.05640.14790.0379-0.02890.08150.01930.0713-4.4276-0.0842-28.4746
51.77530.47350.07212.0002-0.14461.9946-0.03090.06880.1166-0.24250.08930.0120.0632-0.0506-0.05840.13480.0479-0.01530.0399-0.00220.0436-1.72863.7349-45.5247
61.66120.73121.53411.07970.85082.7023-0.01480.06420.04850.02530.05270.1670.1628-0.0644-0.03790.0469-0.0410.00190.09850.03130.0579-14.2963-2.85158.8651
72.324-0.7757-0.50511.8036-0.41561.83840.03980.1701-0.0179-0.14380.0495-0.12580.03560.4303-0.08940.0481-0.0477-0.0050.2492-0.02190.07414.72751.0398.8424
82.59121.11492.20051.91061.93633.0766-0.16630.27130.2056-0.27580.06520.0761-0.32360.14580.10110.1271-0.0841-0.04140.1340.09350.0795-12.56634.1109-4.5
93.7135-1.0648-0.74853.29790.0342.74410.12430.06640.0548-0.1237-0.1198-0.1503-0.14320.0153-0.00460.1701-0.0484-0.06780.08720.06010.0552-14.4776-6.7899-19.048
103.634-0.6904-1.31561.4950.01343.56060.0354-0.3109-0.62120.1057-0.1218-0.0170.68690.05630.08640.3221-0.095-0.16050.08240.10590.2237-16.6166-22.0355-11.1716
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 119
2X-RAY DIFFRACTION2A120 - 202
3X-RAY DIFFRACTION3A203 - 255
4X-RAY DIFFRACTION4A256 - 330
5X-RAY DIFFRACTION5A331 - 433
6X-RAY DIFFRACTION6B1 - 119
7X-RAY DIFFRACTION7B120 - 202
8X-RAY DIFFRACTION8B203 - 255
9X-RAY DIFFRACTION9B256 - 330
10X-RAY DIFFRACTION10B331 - 430

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