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- PDB-3oc7: Crystal structure of an enoyl-CoA hydratase from Mycobacterium avium -

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Basic information

Entry
Database: PDB / ID: 3oc7
TitleCrystal structure of an enoyl-CoA hydratase from Mycobacterium avium
ComponentsEnoyl-CoA hydratase
KeywordsLYASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / non-pathogenic Mycobacterium species / ortholog / Johne's disease in cattle / paratuberculosis / Crohn's disease in humans / hydratase / crotonase / fatty acid metabolism
Function / homology
Function and homology information


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 / 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 ...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 / 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
Enoyl-CoA hydratase / Enoyl-CoA hydratase
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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
DepositionAug 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 6, 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: Enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7352
Polymers27,6731
Non-polymers621
Water4,107228
1
A: Enoyl-CoA hydratase
hetero molecules

A: Enoyl-CoA hydratase
hetero molecules

A: Enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2066
Polymers83,0203
Non-polymers1863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7690 Å2
ΔGint-29 kcal/mol
Surface area30100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.230, 83.230, 93.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Enoyl-CoA hydratase /


Mass: 27673.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: 104 / Gene: MAV_1087 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QBQ2, UniProt: A0A0H2ZTL3*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25.9 mg/mL MyavA.01530.a.A1 PW29874 3C cleaved against JCSG+ condition E11, 0.16 M calcium acetate, 80 mM sodium cacodylate pH 6.5, 14.4% PEG 8000, 20% glycerol, crystal tracking ID ...Details: 25.9 mg/mL MyavA.01530.a.A1 PW29874 3C cleaved against JCSG+ condition E11, 0.16 M calcium acetate, 80 mM sodium cacodylate pH 6.5, 14.4% PEG 8000, 20% glycerol, crystal tracking ID 216676e11, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.928
11K, H, -L20.072
ReflectionResolution: 1.5→50 Å / Num. all: 38839 / Num. obs: 38836 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 20.905 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.5-1.540.4982.7126942896100
1.54-1.580.4253.7150722795100
1.58-1.630.3544.6152442708100
1.63-1.680.2865.7150202665100
1.68-1.730.2416.7143552544100
1.73-1.790.2018142652521100
1.79-1.860.16210133092352100
1.86-1.940.12312.9129812296100
1.94-2.020.09615.8126092239100
2.02-2.120.07919.5118672124100
2.12-2.240.06822.5107121961100
2.24-2.370.0624.1103301909100
2.37-2.540.05327.295591780100
2.54-2.740.0528.788811664100
2.74-30.04830.581121528100
3-3.350.04433.17286139099.9
3.35-3.870.0434.961591202100
3.87-4.740.03836.65402103199.9
4.74-6.710.03536.34369792100
6.710.03338241343999.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.87 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å41.62 Å
Translation3 Å41.62 Å

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Processing

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

3myb


Resolution: 1.5→41.62 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1801 / WRfactor Rwork: 0.1705 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8997 / SU B: 2.477 / SU ML: 0.04 / SU R Cruickshank DPI: 0.0151 / SU Rfree: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.014 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1808 2020 5.2 %RANDOM
Rwork0.1717 ---
obs0.1722 38834 99.9 %-
all-38839 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 56.54 Å2 / Biso mean: 17.6087 Å2 / Biso min: 7.56 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2--1.02 Å20 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 1.5→41.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 4 228 2065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221906
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.9722595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0825263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.72822.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.05115300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3771523
X-RAY DIFFRACTIONr_chiral_restr0.0890.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211458
X-RAY DIFFRACTIONr_mcbond_it0.6291.51264
X-RAY DIFFRACTIONr_mcangle_it1.14422004
X-RAY DIFFRACTIONr_scbond_it2.0853642
X-RAY DIFFRACTIONr_scangle_it3.2684.5584
LS refinement shellResolution: 1.5→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 145 -
Rwork0.229 2699 -
all-2844 -
obs--98.68 %
Refinement TLS params.Method: refined / Origin x: -10.7545 Å / Origin y: 17.0967 Å / Origin z: 0.1777 Å
111213212223313233
T0.0196 Å20.009 Å20.0111 Å2-0.0158 Å20.0053 Å2--0.0329 Å2
L0.1226 °20.0283 °20.0868 °2-0.1518 °2-0.0074 °2--0.0173 °2
S-0.0127 Å °-0.0144 Å °-0.0058 Å °-0.0052 Å °0.0353 Å °0.0077 Å °-0.0169 Å °-0.013 Å °-0.0226 Å °

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