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- PDB-3p5m: Crystal structure of an enoyl-CoA hydratase/isomerase from Mycoba... -

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Basic information

Entry
Database: PDB / ID: 3p5m
TitleCrystal structure of an enoyl-CoA hydratase/isomerase from Mycobacterium avium
ComponentsEnoyl-CoA hydratase/isomerase
KeywordsISOMERASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Coenzyme A / mycobacterium / tuberculosis / non-pathogenic species / ortholog
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/isomerase / Enoyl-CoA hydratase/isomerase
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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
DepositionOct 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Apr 15, 2015Group: Database references
Revision 1.4Sep 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/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)159,7078
Polymers159,5836
Non-polymers1242
Water17,511972
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19670 Å2
ΔGint-143 kcal/mol
Surface area50830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.730, 105.180, 130.980
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: 26597.219 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: 104 / Gene: MAV_2601 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QFV4, UniProt: A0A0H2ZZ96*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 972 / 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: 44.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 19.25 mg/mL protein, 0.2 M K/Na Tartrate, 20% PEG 3350 with 25% ethylene glycol as cryo-protectant, pH 7.5, 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: Aug 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 89524 / Num. obs: 85894 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 20.775 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 11.25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.05-2.10.4143.112945559685.3
2.1-2.160.343.918236609995.7
2.16-2.220.3264.319781612798.9
2.22-2.290.3035.116874553891.5
2.29-2.370.2295.719023581599.6
2.37-2.450.2215.818510564999.5
2.45-2.540.1876.817956544799.6
2.54-2.650.1717.217330523699.4
2.65-2.760.1647.716617502698.4
2.76-2.90.1298.715938476098.9
2.9-3.060.1051015418456398.4
3.06-3.240.08711.414612428898.1
3.24-3.470.07814.913446397896.5
3.47-3.740.06220.212315368395.1
3.74-4.10.05125.111027332093.2
4.1-4.580.03532.610667308595.7
4.58-5.290.03729.89432270994.4
5.29-6.480.04623.28045229993.7
6.48-9.170.0333.56200178192.1
9.170.02149.7301289579

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 58.84 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.93 Å
Translation3 Å19.93 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 3gow

3gow
PDB Unreleased entry


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.1952 / WRfactor Rwork: 0.1463 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8523 / SU B: 9.934 / SU ML: 0.121 / SU R Cruickshank DPI: 0.2211 / SU Rfree: 0.1891 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 4306 5 %RANDOM
Rwork0.1769 ---
obs0.1797 85638 95.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.36 Å2 / Biso mean: 16.4799 Å2 / Biso min: 6.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.15 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10761 0 8 972 11741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02211068
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.96815096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73251540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.09723.123413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.688151656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0291588
X-RAY DIFFRACTIONr_chiral_restr0.0990.21804
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218406
X-RAY DIFFRACTIONr_mcbond_it0.6951.57489
X-RAY DIFFRACTIONr_mcangle_it1.232211848
X-RAY DIFFRACTIONr_scbond_it2.33933579
X-RAY DIFFRACTIONr_scangle_it3.8934.53222
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 285 -
Rwork0.263 5285 -
all-5570 -
obs--85.08 %
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)
10.7888-0.21350.03930.39850.18130.534-0.0415-0.0763-0.00680.07850.02260.02120.0362-0.00690.01880.0808-0.01350.00010.087-0.00110.04981.300112.274733.1463
20.1264-0.43-0.39862.3291-0.03320.9298-0.140.0474-0.06940.3920.0780.0971-0.1840.07340.0620.1677-0.00370.00180.0785-0.00960.05711.95626.00525.474
30.2351-0.04370.12240.1569-0.02010.18390.029-0.0167-0.0067-0.0135-0.00050.00770.0139-0.0104-0.02850.0796-0.00930.00570.0849-0.01130.0691-1.72179.787817.1092
40.9279-0.51160.23581.0346-0.03940.2799-0.0051-0.08850.11070.1121-0.0313-0.0057-0.05480.0020.03640.0925-0.00610.01860.0557-0.03020.0481-4.868829.070117.2229
55.7661-1.8188-5.83360.58522.368310.99740.14280.68970.6527-0.1086-0.2647-0.1965-0.7113-1.53830.12190.05230.0866-0.03170.11930.00610.2322-14.902836.6924-11.603
60.9912-0.5575-1.09190.25740.39673.93610.22430.2060.5191-0.2003-0.1004-0.1455-0.2435-0.1767-0.1240.09030.01630.02120.00780.09360.2386-8.006534.154-12.9392
70.26260.05890.01910.26180.10930.1176-0.0330.02830.0582-0.01810.01370.02210.0169-0.00250.01930.0739-0.0053-0.00790.07140.00820.0863-5.188621.246-6.9582
80.29820.1999-0.44040.65150.18132.0922-0.03070.07080.1175-0.08360.10210.0252-0.0638-0.0147-0.07140.0592-0.01220.01090.0630.04260.081510.536819.4339-21.3072
90.8525-1.20380.41.6245-0.85321.30250.0313-0.01270.0688-0.1782-0.019-0.24650.1380.1582-0.01230.04520.00030.06060.0712-0.02190.126826.4217-3.871-10.0642
100.1677-0.0664-0.04650.2679-0.01580.3627-0.0098-0.00870.0181-0.0090.011-0.02610.03120.0084-0.00110.0681-0.0010.00910.077-0.00320.076613.24290.9004-2.7747
110.6949-0.44950.592.2185-2.48683.97420.07740.07170.0864-0.1385-0.1308-0.07490.26420.49220.05340.04730.0633-0.01810.1131-0.02570.044724.39151.453815.3754
120.9245-4.47530.00138.4731-2.99013.93730.331-0.1942-0.0262-0.6358-0.08960.6310.7440.108-0.24140.20.0143-0.08710.0275-0.01640.041219.2642-10.095323.4361
130.8686-0.4853-0.11440.5189-0.20821.2977-0.0248-0.173-0.00890.13310.0210.1219-0.0364-0.01470.00390.0678-0.01980.04480.0832-0.01770.067-36.0797-7.907324.4363
140.3443-0.08230.02630.2232-0.18350.13990.0321-0.00660.01780.0224-0.02350.0147-0.00010.0059-0.00870.0735-0.0090.00310.0831-0.00440.0721-26.9175-9.512312.4124
152.2901-0.33311.11230.5563-0.50530.645-0.056-0.1373-0.03450.00380.06330.04270.0343-0.0977-0.00730.08380.00560.00330.0870.01470.0558-23.6298-29.071220.5015
161.64781.50220.64291.51131.31142.9864-0.04480.03390.0771-0.0770.0581-0.01-0.03370.0565-0.01320.06450.025-0.01850.07980.0240.0698-10.1058-28.868726.3408
170.72630.071-0.64480.593-0.75122.5985-0.0371-0.0125-0.1184-0.02630.0098-0.070.14490.02860.02730.06370.0132-0.00410.0397-0.0170.0958-4.3986-36.557-2.0592
182.1503-0.81882.08560.27850.25783.6733-0.03320.21290.16810.0297-0.13130.17490.25660.22390.16450.1004-0.0081-0.01320.0829-0.01690.1352-4.9363-29.0873-14.6119
190.1622-0.0997-0.07220.1201-0.06930.23140.00180.0017-0.0189-0.0142-0.00940.00480.00140.01080.00770.0795-0.00650.00110.0741-0.00160.0797-11.9416-22.292-3.2232
201.1494-1.1632-0.82961.17251.43821.21090.02630.09250.01310.00840.0498-0.03370.31830.0751-0.07610.15820.0005-0.0130.0542-0.02790.0265-16.0123-24.8963-25.3362
210.6227-0.3032-0.05470.97760.05650.5975-0.01860.09570.0502-0.04720.00330.0137-0.0255-0.04220.01530.0867-0.0103-0.02490.07430.01040.0507-33.7963-1.5259-26.7463
220.16120.0814-0.09370.1537-0.0970.37880.01040.03330.0412-0.01110.01030.0327-0.0116-0.0313-0.02080.0772-0.0083-0.02160.07850.00110.0824-32.7366-2.3056-14.6773
230.0895-0.0231-0.05270.24690.00620.245-0.0020.0011-0.00290.00110.03040.0077-0.00530.0313-0.02840.0751-0.0068-0.01670.0808-0.00290.0729-24.8087-5.7688-11.3022
240.62010.0349-0.32122.57640.95881.11070.00950.08080.0955-0.09890.06060.2061-0.0367-0.0458-0.07020.01660.00820.00160.06430.04650.1127-46.19793.7075-1.9461
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 62
2X-RAY DIFFRACTION2A63 - 82
3X-RAY DIFFRACTION3A83 - 202
4X-RAY DIFFRACTION4A203 - 251
5X-RAY DIFFRACTION5B0 - 11
6X-RAY DIFFRACTION6B12 - 45
7X-RAY DIFFRACTION7B46 - 209
8X-RAY DIFFRACTION8B210 - 251
9X-RAY DIFFRACTION9C-3 - 45
10X-RAY DIFFRACTION10C46 - 211
11X-RAY DIFFRACTION11C212 - 240
12X-RAY DIFFRACTION12C241 - 251
13X-RAY DIFFRACTION13D0 - 69
14X-RAY DIFFRACTION14D70 - 211
15X-RAY DIFFRACTION15D212 - 241
16X-RAY DIFFRACTION16D242 - 251
17X-RAY DIFFRACTION17E1 - 56
18X-RAY DIFFRACTION18E57 - 70
19X-RAY DIFFRACTION19E71 - 211
20X-RAY DIFFRACTION20E212 - 251
21X-RAY DIFFRACTION21F-1 - 58
22X-RAY DIFFRACTION22F59 - 126
23X-RAY DIFFRACTION23F127 - 213
24X-RAY DIFFRACTION24F214 - 251

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