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- PDB-5go2: Crystal structure of chorismate mutase like domain of bifunctiona... -

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Basic information

Entry
Database: PDB / ID: 5go2
TitleCrystal structure of chorismate mutase like domain of bifunctional DAHP synthase of Bacillus subtilis in complex with Citrate
ComponentsProtein AroA(G)
KeywordsISOMERASE / Type II chorismate mutase / CML domain / Bifunctional DAHP synthase / citrate / bacillus subtilis
Function / homology
Function and homology information


chorismate mutase / chorismate mutase activity / 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / aldehyde-lyase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
Chorismate mutase, Firmicutes/Deinococcus / Phospho-2-dehydro-3-deoxyheptonate aldolase, subtype 2 / Chorismate mutase / Chorismate mutase domain superfamily / Chorismate Mutase Domain, subunit A / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Chorismate mutase domain profile. / Chorismate mutase type II / DAHP synthetase I/KDSA ...Chorismate mutase, Firmicutes/Deinococcus / Phospho-2-dehydro-3-deoxyheptonate aldolase, subtype 2 / Chorismate mutase / Chorismate mutase domain superfamily / Chorismate Mutase Domain, subunit A / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Chorismate mutase domain profile. / Chorismate mutase type II / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase-type TIM barrel / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / Protein AroA(G)
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.907 Å
AuthorsPratap, S. / Dev, A. / Sharma, V. / Yadav, R. / Narwal, M. / Tomar, S. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Council for scientific and industrial research37(1580)/13/EMR-II dated 21-03-2013 India
CitationJournal: Sci Rep / Year: 2017
Title: Structure of Chorismate Mutase-like Domain of DAHPS from Bacillus subtilis Complexed with Novel Inhibitor Reveals Conformational Plasticity of Active Site.
Authors: Pratap, S. / Dev, A. / Kumar, V. / Yadav, R. / Narwal, M. / Tomar, S. / Kumar, P.
History
DepositionJul 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein AroA(G)
B: Protein AroA(G)
C: Protein AroA(G)
D: Protein AroA(G)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,78013
Polymers41,7234
Non-polymers1,0579
Water2,216123
1
A: Protein AroA(G)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6233
Polymers10,4311
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area7190 Å2
MethodPISA
2
B: Protein AroA(G)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8154
Polymers10,4311
Non-polymers3843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7140 Å2
MethodPISA
3
C: Protein AroA(G)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6233
Polymers10,4311
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area7100 Å2
MethodPISA
4
D: Protein AroA(G)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7193
Polymers10,4311
Non-polymers2882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.090, 45.430, 48.320
Angle α, β, γ (deg.)81.65, 82.88, 78.25
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Protein AroA(G)


Mass: 10430.755 Da / Num. of mol.: 4
Fragment: Chorismate Mutase type II like domain, UNP residues 1-90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: aroA, BSU29750
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P39912, chorismate mutase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M Potassium sodium tartrate tetrahydrate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 2.0M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.907→24.67 Å / Num. obs: 26625 / % possible obs: 93 % / Redundancy: 3.1 % / Net I/σ(I): 19.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GMU

5gmu


Resolution: 1.907→24.665 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.99
RfactorNum. reflection% reflection
Rfree0.2332 1251 4.72 %
Rwork0.1832 --
obs0.1856 26509 91.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.907→24.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2817 0 61 123 3001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072893
X-RAY DIFFRACTIONf_angle_d0.763882
X-RAY DIFFRACTIONf_dihedral_angle_d12.7081820
X-RAY DIFFRACTIONf_chiral_restr0.044428
X-RAY DIFFRACTIONf_plane_restr0.004519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9071-1.98340.35721430.33652465X-RAY DIFFRACTION81
1.9834-2.07370.31651410.25712769X-RAY DIFFRACTION91
2.0737-2.18290.25771140.21212808X-RAY DIFFRACTION91
2.1829-2.31960.30691440.212744X-RAY DIFFRACTION91
2.3196-2.49860.26371480.19082850X-RAY DIFFRACTION93
2.4986-2.74970.22081220.18612834X-RAY DIFFRACTION93
2.7497-3.14690.24521560.18682845X-RAY DIFFRACTION94
3.1469-3.96210.22111410.15412951X-RAY DIFFRACTION97
3.9621-24.66740.19181420.16872992X-RAY DIFFRACTION97
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)
15.28624.17320.84753.5440.55890.3464-0.0107-0.121-0.10440.1935-0.01120.09380.07220.060.00350.2880.0808-0.00250.30070.04340.31935.1502-3.08754.4632
21.76172.7392.20619.94725.55825.8772-0.25531.0913-0.782-1.69011.1813-0.14320.72990.0469-0.85760.56270.1266-0.04570.8345-0.09710.6312-20.6325-8.0836-7.5798
35.27374.17134.8223.26423.81874.40550.24330.07270.72130.6121-0.16910.24910.66950.38040.08210.32680.11230.06830.40530.02620.5049-14.26056.9217-1.1992
47.35554.61671.18827.70760.38562.3306-0.04630.61670.5533-0.28750.20650.27910.02850.1434-0.09040.26730.136-0.00160.38550.0650.303-5.11183.7464-4.0233
57.96285.0034-1.97684.6164-1.85291.36920.12870.04080.2630.2787-0.00520.2318-0.07890.0073-0.15640.24160.10430.04050.21620.0050.2581-1.68362.81474.7449
67.09672.1476-2.24230.59-0.50653.394-0.0378-0.1913-0.4866-0.2462-0.3773-0.14180.25630.5610.37560.30710.13280.00560.38370.05220.37814.9153-2.0312-5.1197
75.22744.7006-1.05745.6465-0.56991.0378-0.08170.1746-0.3223-0.3578-0.0977-0.18690.1374-0.05590.12890.2930.07880.0020.37990.04890.31654.6169-1.2567-5.9776
82.79351.9943-2.38882.5746-1.84721.9170.1310.12850.1065-0.00730.0150.1109-0.1605-0.0953-0.18380.27310.0589-0.02220.31880.06280.2859-17.829520.887519.2099
98.15241.97584.49334.96882.1998.9497-0.7835-1.2157-0.6647-0.02530.3650.69450.9895-0.56510.31530.6365-0.05410.05160.49630.10020.8803-26.6279-1.892529.013
108.33334.9676-3.97877.3661-2.54138.54070.15120.3643-1.0062-0.84070.0888-0.19581.677-0.9699-0.28290.8586-0.0534-0.11980.41840.08340.4891-11.04613.065824.5571
115.73741.117-1.47885.7639-0.09542.4595-0.1413-0.1125-0.28230.2142-0.1556-0.31390.2265-0.08890.28930.38280.0389-0.01360.27370.04420.2309-13.895911.640228.0316
128.22917.7563.57416.85012.79060.80350.10270.0978-0.12570.0523-0.0935-0.14320.08460.1311-0.05580.32150.05820.02460.36350.04190.343-12.47914.435318.2966
138.29757.71271.95257.50681.43253.19870.129-0.01930.02780.3297-0.1233-0.0482-0.4029-0.14260.0180.39230.1284-0.02770.34710.03620.4474-15.940130.336427.1947
144.34135.863-1.94188.7874-1.29152.77720.4713-0.7814-0.16870.8865-0.3849-0.2674-0.070.1866-0.01450.46540.0536-0.04380.28120.01980.2474-12.065522.970530.235
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 47 )
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 60 )
4X-RAY DIFFRACTION4chain 'A' and (resid 61 through 86 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 41 )
6X-RAY DIFFRACTION6chain 'B' and (resid 42 through 61 )
7X-RAY DIFFRACTION7chain 'B' and (resid 62 through 88 )
8X-RAY DIFFRACTION8chain 'C' and (resid 2 through 40 )
9X-RAY DIFFRACTION9chain 'C' and (resid 41 through 47 )
10X-RAY DIFFRACTION10chain 'C' and (resid 48 through 61 )
11X-RAY DIFFRACTION11chain 'C' and (resid 62 through 88 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 40 )
13X-RAY DIFFRACTION13chain 'D' and (resid 41 through 67 )
14X-RAY DIFFRACTION14chain 'D' and (resid 68 through 87 )

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