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- PDB-3tlf: Crystal structure of an enoyl-CoA hydratase/isomerase from Mycoba... -

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Basic information

Entry
Database: PDB / ID: 3tlf
TitleCrystal structure of an enoyl-CoA hydratase/isomerase from Mycobacterium paratuberculosis
Componentsenoyl-CoA hydratase/isomerase
KeywordsISOMERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / otholog / enoyl-CoA isomerase/hydratase family protein / fatty acid biosynthesis / metabolism / unsaturated fatty acids
Function / homology
Function and homology information


enoyl-CoA hydratase activity
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
Uncharacterized protein
Similarity search - Component
Biological speciesMycobacterium avium subsp. paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 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 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 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: enoyl-CoA hydratase/isomerase
B: enoyl-CoA hydratase/isomerase
C: enoyl-CoA hydratase/isomerase
D: enoyl-CoA hydratase/isomerase
E: enoyl-CoA hydratase/isomerase
F: enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,37517
Polymers182,6926
Non-polymers68311
Water16,754930
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35610 Å2
ΔGint-143 kcal/mol
Surface area49610 Å2
MethodPISA
2
A: enoyl-CoA hydratase/isomerase
B: enoyl-CoA hydratase/isomerase
C: enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6568
Polymers91,3463
Non-polymers3105
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12880 Å2
ΔGint-54 kcal/mol
Surface area29270 Å2
MethodPISA
3
D: enoyl-CoA hydratase/isomerase
E: enoyl-CoA hydratase/isomerase
F: enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7189
Polymers91,3463
Non-polymers3726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13300 Å2
ΔGint-49 kcal/mol
Surface area29770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.740, 140.500, 148.760
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
enoyl-CoA hydratase/isomerase


Mass: 30448.654 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria)
Gene: MAP_2398 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli)
References: UniProt: Q73XB1, Delta3-Delta2-enoyl-CoA isomerase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 930 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: MypaA.01530.c.A1 PW29510 at 27.56 mg/mL against PACT C10, 0.2 M MgCl2, 0.1 M Hepes pH 7.0, 20% PEG 6000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 217910c10, VAPOR ...Details: MypaA.01530.c.A1 PW29510 at 27.56 mg/mL against PACT C10, 0.2 M MgCl2, 0.1 M Hepes pH 7.0, 20% PEG 6000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 217910c10, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 89246 / Num. obs: 88344 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Biso Wilson estimate: 31.403 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 19.15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.15-2.210.4685.2567272651699.9
2.21-2.270.4646.0555682612496.4
2.27-2.330.4416.0767039601596.9
2.33-2.40.3288.12734416009100
2.4-2.480.2979.4779983580799.8
2.48-2.570.27310.4581917563999.8
2.57-2.670.25811.3177921545399.7
2.67-2.780.22412.6475469525199.7
2.78-2.90.17614.5673426501999.9
2.9-3.040.13418.1670814483099.7
3.04-3.210.11820.3967496460699.7
3.21-3.40.09525.563026432599.2
3.4-3.630.09329.6456134407499.3
3.63-3.930.07236.5948568380098.4
3.93-4.30.05743.1548647347998.3
4.3-4.810.0548.4544796317498.5
4.81-5.550.05641.2540704284198.6
5.55-6.80.06636.2734323240298.9
6.8-9.620.04450.626080189898.2
9.620.03859.3513510108295.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 56.6 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å24.12 Å
Translation3 Å24.12 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 3r0o
Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.1848 / WRfactor Rwork: 0.1542 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8591 / SU B: 8.636 / SU ML: 0.118 / SU R Cruickshank DPI: 0.2478 / SU Rfree: 0.1861 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 4427 5 %RANDOM
Rwork0.1813 ---
obs0.1831 88343 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.52 Å2 / Biso mean: 25.8369 Å2 / Biso min: 10.52 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å20 Å2
2---0.66 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11746 0 44 930 12720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01912054
X-RAY DIFFRACTIONr_bond_other_d0.0090.028045
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.95616407
X-RAY DIFFRACTIONr_angle_other_deg1.522319512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62851529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32622.981540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18151903
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.58315117
X-RAY DIFFRACTIONr_chiral_restr0.0860.21897
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02113541
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022492
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 308 -
Rwork0.193 5826 -
all-6134 -
obs--99.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.1404-0.04570.06610.3423-0.22130.19910.0323-0.0148-0.007-0.0849-0.02640.00260.03540.0132-0.00580.10380.0201-0.0010.02740.00270.00610.6414-10.834435.8365
20.09140.1299-0.03740.2095-0.14510.6702-0.0042-0.0097-0.0016-0.01390.0102-0.0119-0.0763-0.1649-0.00610.07230.04750.00660.07120.00090.0121-15.560415.46644.4629
30.1327-0.22890.05530.4489-0.16580.2996-0.00940.02560.0460.0494-0.054-0.1333-0.05250.0320.06340.076-0.0289-0.02430.01460.01910.074815.964914.201647.8689
40.3358-0.0212-0.04270.2354-0.16980.3376-0.06030.0286-0.1008-0.04210.039-0.0450.01790.00080.02130.0554-0.00980.01410.0327-0.01750.06-3.2142-23.993566.6909
50.1436-0.0778-0.00220.3769-0.05310.0906-0.01120.00540.02310.0363-0.0185-0.0993-0.0478-0.01270.02970.0595-0.0059-0.02450.02990.00480.055412.03080.072979.4185
60.19750.19160.0870.24960.04010.3565-0.0017-0.0133-0.005-0.0233-0.00120.0204-0.0839-0.12270.00290.06740.05770.00420.07050.00810.0242-19.92012.023976.6437
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999
5X-RAY DIFFRACTION5E-10 - 9999
6X-RAY DIFFRACTION6F-10 - 9999

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