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- PDB-3r9s: Structure of a carnitinyl-CoA dehydratase from Mycobacterium avium 104 -

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Basic information

Entry
Database: PDB / ID: 3r9s
TitleStructure of a carnitinyl-CoA dehydratase from Mycobacterium avium 104
ComponentsCarnitinyl-CoA dehydratase
KeywordsLYASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease / carnitinyl-CoA dehydratase
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Hydro-lyases / enoyl-CoA hydratase activity / fatty acid beta-oxidation
Similarity search - Function
Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BENZOIC ACID / Carnitinyl-CoA dehydratase / Carnitinyl-CoA dehydratase
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionMar 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: 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 / 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: Carnitinyl-CoA dehydratase
B: Carnitinyl-CoA dehydratase
C: Carnitinyl-CoA dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9849
Polymers84,4923
Non-polymers4936
Water8,161453
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-15 kcal/mol
Surface area27570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.740, 74.961, 76.982
Angle α, β, γ (deg.)90.00, 112.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carnitinyl-CoA dehydratase


Mass: 28163.941 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: 104 / Gene: MAV_1277 / Production host: Escherichia coli (E. coli)
References: UniProt: A0QC84, UniProt: A0A0H2ZTH2*PLUS, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.42 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, cryoprotectant: 25% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 23, 2011
RadiationMonochromator: asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 40794 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.095 / Χ2: 1.008 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.243.70.37420460.962199.8
2.24-2.283.70.33720051.06199.4
2.28-2.323.70.3120241.034199.7
2.32-2.373.70.28320341.055199.7
2.37-2.423.70.24720241.046199.8
2.42-2.483.70.23320551.069199.5
2.48-2.543.80.21819841.046199.8
2.54-2.613.80.19820541.034199.6
2.61-2.693.70.18220461.034199.6
2.69-2.773.70.16220241.007199.3
2.77-2.873.70.1420311.01199.4
2.87-2.993.70.12620541.017199.6
2.99-3.123.70.11420250.927199.7
3.12-3.293.70.09720480.93199.2
3.29-3.493.70.08820230.924198.9
3.49-3.763.70.08520220.953199
3.76-4.143.60.07720370.956198.9
4.14-4.743.60.07120620.949199
4.74-5.973.60.06120811.048199.6
5.97-503.70.04321151.0791100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.48 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.68 Å
Translation2.5 Å48.68 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3R0O

3r0o


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2348 / WRfactor Rwork: 0.1789 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.855 / SU B: 11.459 / SU ML: 0.133 / SU R Cruickshank DPI: 0.2531 / SU Rfree: 0.2012 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 2051 5 %RANDOM
Rwork0.1742 ---
obs0.1768 40699 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 88.72 Å2 / Biso mean: 43.6708 Å2 / Biso min: 22.72 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å20.57 Å2
2---1.71 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5518 0 34 453 6005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225695
X-RAY DIFFRACTIONr_bond_other_d0.0010.023701
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9677767
X-RAY DIFFRACTIONr_angle_other_deg0.92139010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.685780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85323.498223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57215813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7781548
X-RAY DIFFRACTIONr_chiral_restr0.0710.2901
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021127
X-RAY DIFFRACTIONr_mcbond_it0.5381.53847
X-RAY DIFFRACTIONr_mcbond_other0.1191.51584
X-RAY DIFFRACTIONr_mcangle_it1.00226045
X-RAY DIFFRACTIONr_scbond_it1.73431848
X-RAY DIFFRACTIONr_scangle_it2.7974.51715
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 153 -
Rwork0.211 2798 -
all-2951 -
obs--98.43 %
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)
10.7764-0.0218-0.06430.2174-0.05540.76020.00120.03780.0074-0.03360.01410.06560.0164-0.075-0.01530.008-0.0055-0.01890.02430.00990.0487-19.0221-7.6007-31.2107
21.3021-0.1903-0.52610.6242-0.29410.7563-0.0392-0.12650.01590.10040.0111-0.0613-0.01250.10320.02810.0259-0.0048-0.00720.0419-0.00630.0072-2.5321-16.6684-3.8619
31.0532-0.16940.12990.9420.07030.6458-0.00360.07630.0133-0.1502-0.0094-0.019-0.00480.06560.0130.02530.00130.00370.03860.01350.005915.2195-11.7255-31.7657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 263
2X-RAY DIFFRACTION2B4 - 263
3X-RAY DIFFRACTION3C4 - 263

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