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- PDB-5yiy: Crystal structure of D175A mutant of Rv3272 from Mycobacterium tu... -

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Basic information

Entry
Database: PDB / ID: 5yiy
TitleCrystal structure of D175A mutant of Rv3272 from Mycobacterium tuberculosis
ComponentsCoA transferase
KeywordsTRANSFERASE / CoA transferases / D175A / Rv3272 / Mycobacterium
Function / homologyTransferases; Transferring sulfur-containing groups; CoA-transferases / : / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III domain 3 superfamily / CoA-transferase family III / transferase activity / Probable fatty acyl-CoA transferase Rv3272
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.504 Å
AuthorsKarade, S.S. / Pratap, J.V.
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2019
Title: Rv3272 encodes a novel Family III CoA transferase that alters the cell wall lipid profile and protects mycobacteria from acidic and oxidative stress.
Authors: Karade, S.S. / Pandey, S. / Ansari, A. / Das, S. / Tripathi, S. / Arora, A. / Chopra, S. / Pratap, J.V. / Dasgupta, A.
History
DepositionOct 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_volume ..._audit_author.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CoA transferase
B: CoA transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9583
Polymers84,9232
Non-polymers351
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12080 Å2
ΔGint-92 kcal/mol
Surface area27390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.678, 78.678, 251.475
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CoA transferase


Mass: 42461.438 Da / Num. of mol.: 2 / Mutation: D175A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv3272 / Production host: Escherichia coli (E. coli) / References: UniProt: P96877
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.2 Å3/Da / Density % sol: 44.07 % / Description: Rod shaped crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris pH 8.5, 100mM MgCl2, PEG 4000, 20-25% PEG 6000, 100um Octanoyl CoA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.498→75.099 Å / Num. obs: 28431 / % possible obs: 94.23 % / Redundancy: 4.2 % / Biso Wilson estimate: 47.59 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.08823 / Rrim(I) all: 0.09973 / Net I/σ(I): 9.94
Reflection shellResolution: 2.504→2.594 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.4417 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 1755 / CC1/2: 0.726 / % possible all: 63.06

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000v715.5data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.504→49.115 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2345 1350 5.07 %
Rwork0.202 --
obs0.2037 26601 94.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.504→49.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5399 0 1 142 5542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095511
X-RAY DIFFRACTIONf_angle_d0.9927529
X-RAY DIFFRACTIONf_dihedral_angle_d14.4791975
X-RAY DIFFRACTIONf_chiral_restr0.068886
X-RAY DIFFRACTIONf_plane_restr0.006998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5043-2.59380.3312810.30061669X-RAY DIFFRACTION63
2.5938-2.69760.30081150.26422152X-RAY DIFFRACTION82
2.6976-2.82040.28281200.25812554X-RAY DIFFRACTION97
2.8204-2.96910.27811550.23172595X-RAY DIFFRACTION100
2.9691-3.1550.25081420.22172656X-RAY DIFFRACTION100
3.155-3.39860.23781220.20892668X-RAY DIFFRACTION100
3.3986-3.74050.24631640.19632637X-RAY DIFFRACTION100
3.7405-4.28150.2241620.17922668X-RAY DIFFRACTION100
4.2815-5.39310.19151650.16872710X-RAY DIFFRACTION100
5.3931-49.12410.20311240.18562942X-RAY DIFFRACTION100
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)
11.38740.6693-0.39922.9527-0.49173.1818-0.0046-0.37490.07170.2416-0.09630.0773-0.1627-0.02310.06840.27190.02050.00120.3725-0.11740.3056-7.5722-30.4415-11.1217
21.0091-0.0344-0.25683.586-0.0383.27360.0719-0.28360.01410.0756-0.27080.61830.2876-0.65760.11350.2581-0.0683-0.00920.4581-0.11050.386-17.0789-41.8809-14.9091
32.1327-0.4049-0.31662.2369-0.20561.9659-0.2016-0.001-0.14040.0049-0.03160.0610.2085-0.12340.14950.2297-0.0280.01230.2403-0.02820.2105-3.8545-42.9202-27.6935
44.91121.5575-0.98531.2932-0.29162.0802-0.2781-0.2364-0.1475-0.3630.0196-0.20180.2642-0.22740.17870.44130.0730.08140.26430.01250.358916.0431-41.9543-48.8213
54.27711.79760.1696.3151-0.75323.50330.05170.5552-0.0402-0.78380.35630.84840.9242-0.34290.03870.5384-0.01580.04490.2704-0.04780.431915.6181-48.4751-57.5673
62.2-0.2298-1.48151.37350.15022.9790.0264-0.31820.07580.07260.0736-0.07010.20940.4097-0.10480.23130.0131-0.02020.2789-0.01350.366218.9382-33.7932-38.3376
71.1023-0.782-0.63830.8080.82540.89060.0433-0.27250.17760.2497-0.0577-0.1221-0.20620.3363-0.18830.4258-0.03850.01310.3386-0.08470.3986-1.2103-21.4979-14.4584
81.79940.6088-0.48162.1266-0.73482.7009-0.01220.15950.194-0.4054-0.01140.02150.0623-0.42820.00760.33580.0746-0.08370.3442-0.01830.3193-9.478-31.9753-48.0314
91.9318-0.0243-0.17891.1174-0.42451.6544-0.0206-0.06820.2794-0.1466-0.0356-0.0085-0.1865-0.05870.09030.30010.00610.01530.2522-0.03750.26142.3573-28.8344-36.0548
100.85741.4497-0.02225.0624-0.43131.60050.1672-0.54280.04080.2646-0.337-0.11590.0727-0.18460.20710.27060.04670.01860.43460.02680.30417.5315-53.7305-11.0223
114.68931.96020.82636.77320.99852.6440.001-0.45020.46140.6791-0.2254-0.2089-0.320.55010.43390.4945-0.0303-0.10350.37010.06020.384114.5048-51.3737-2.9175
121.7787-0.89680.80691.8742-1.25252.23930.0899-0.1025-0.4062-0.19690.0610.15180.3161-0.2515-0.05760.3274-0.01730.0740.2492-0.03050.3526-0.3361-57.7372-22.3416
130.8368-0.45660.51231.208-0.67070.93720.01160.4189-0.1883-0.55560.07470.37640.2658-0.6769-0.25390.3889-0.0048-0.1080.5822-0.07680.3686-16.4363-39.1521-43.6871
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 106 )
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 145 )
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 222 )
4X-RAY DIFFRACTION4chain 'A' and (resid 223 through 277 )
5X-RAY DIFFRACTION5chain 'A' and (resid 278 through 298 )
6X-RAY DIFFRACTION6chain 'A' and (resid 299 through 355 )
7X-RAY DIFFRACTION7chain 'A' and (resid 356 through 394 )
8X-RAY DIFFRACTION8chain 'B' and (resid 5 through 106 )
9X-RAY DIFFRACTION9chain 'B' and (resid 107 through 222 )
10X-RAY DIFFRACTION10chain 'B' and (resid 223 through 277 )
11X-RAY DIFFRACTION11chain 'B' and (resid 278 through 298 )
12X-RAY DIFFRACTION12chain 'B' and (resid 299 through 359 )
13X-RAY DIFFRACTION13chain 'B' and (resid 360 through 393 )

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