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- PDB-3r0o: Crystal structure of carnitinyl-CoA hydratase from Mycobacterium avium -

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Basic information

Entry
Database: PDB / ID: 3r0o
TitleCrystal structure of carnitinyl-CoA hydratase from Mycobacterium avium
ComponentsCarnitinyl-CoA dehydratase
KeywordsLYASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / fatty acid biosynthesis / FAB / coenzyme A / ortholog
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Hydro-lyases / enoyl-CoA hydratase / 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
: / Probable enoyl-CoA hydratase EchA17 / Carnitinyl-CoA dehydratase
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
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: Carnitinyl-CoA dehydratase
B: Carnitinyl-CoA dehydratase
C: Carnitinyl-CoA dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,11910
Polymers86,6783
Non-polymers4427
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-18 kcal/mol
Surface area29550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.890, 105.610, 109.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carnitinyl-CoA dehydratase / carnitinyl-CoA hydratase


Mass: 28892.646 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: 104 / Gene: MAV_2597 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli)
References: UniProt: A0QFV0, UniProt: A0A0H2ZXF2*PLUS, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 564 / 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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: MyavA.01530.a.A1 PW29034 at 26.76 mg/mL against JCSG+ screen condition D12: 40 mM potassium phosphate monobasic, 15% PEG8000, 20% glycerol, crystal tracking ID 216675d12, pH 7.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 27, 2010 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 54122 / Num. obs: 52876 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 12.78
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.1-2.1520.2892.9363123967318280.2
2.15-2.210.2553.587888360193.6
2.21-2.280.2434.4810188371199.3
2.28-2.350.2155.7912425365299.6
2.35-2.420.1876.6212389351099.8
2.42-2.510.1757.0612024339399.8
2.51-2.60.1557.911810331399.8
2.6-2.710.1368.5711405319599.8
2.71-2.830.111010896304899.9
2.83-2.970.09211.6310540292999.9
2.97-3.130.08113.2610056279899.9
3.13-3.320.06416.629441263799.8
3.32-3.550.05220.778937248499.7
3.55-3.830.04424.68239230999.7
3.83-4.20.03827.477693215599.4
4.2-4.70.03429.956906194399.5
4.7-5.420.03727.866170173599.7
5.42-6.640.03824.885295150399.7
6.64-9.390.03130.763971113397.2
9.390.02435.95214664592.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.13 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å29.61 Å
Translation3 Å29.61 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QXI

3qxi


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.1942 / WRfactor Rwork: 0.1503 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8685 / SU B: 9.188 / SU ML: 0.11 / SU R Cruickshank DPI: 0.1853 / SU Rfree: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 2665 5.1 %RANDOM
Rwork0.1694 ---
obs0.1718 52700 97.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.97 Å2 / Biso mean: 21.3216 Å2 / Biso min: 4 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å20 Å20 Å2
2--0.67 Å20 Å2
3---1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5733 0 27 564 6324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225880
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.9618014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5025790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67423.908238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47915876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1261545
X-RAY DIFFRACTIONr_chiral_restr0.0860.2930
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214504
X-RAY DIFFRACTIONr_mcbond_it0.6411.53898
X-RAY DIFFRACTIONr_mcangle_it1.17426180
X-RAY DIFFRACTIONr_scbond_it2.11731982
X-RAY DIFFRACTIONr_scangle_it3.5674.51830
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 154 -
Rwork0.212 3020 -
all-3174 -
obs--80.15 %
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)
10.6757-0.0019-0.09130.56240.30540.40190.0031-0.04970.04060.0980.0026-0.02220.035-0.0462-0.00570.02570.007-0.01370.02680.00050.022-23.8756-10.994642.2305
20.30710.0839-0.01230.60450.18870.5274-0.01160.03250.0246-0.02510.0464-0.0394-0.00790.036-0.03480.0030.0029-0.0040.02760.00570.0407-3.8536-13.604814.8146
30.2980.10570.06350.25750.09890.59530.0436-0.006-0.05460.0064-0.02840.00510.0679-0.0333-0.01520.014-0.0017-0.01420.01930.01150.0438-28.6068-37.082320.2532
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 269
2X-RAY DIFFRACTION2B9 - 269
3X-RAY DIFFRACTION3C8 - 269

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