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- PDB-3qka: Crystal structure of enoyl-CoA hydratase EchA5 from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 3qka
TitleCrystal structure of enoyl-CoA hydratase EchA5 from Mycobacterium marinum
ComponentsEnoyl-CoA hydratase, EchA5
KeywordsLYASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / tuberculosis / ortholog / enoyl-CoA / hydratase / isomerase / acyl-CoA / fatty acid metabolism / NAD / NADH
Function / homology
Function and homology information


enoyl-CoA hydratase activity
Similarity search - Function
Helix Hairpins - #2460 / 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 / Helix Hairpins / Alpha-Beta Complex ...Helix Hairpins - #2460 / 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 / Helix Hairpins / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Enoyl-CoA hydratase, EchA5
Similarity search - Component
Biological speciesMycobacterium marinum M (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
DepositionJan 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-CoA hydratase, EchA5
B: Enoyl-CoA hydratase, EchA5
C: Enoyl-CoA hydratase, EchA5
D: Enoyl-CoA hydratase, EchA5
E: Enoyl-CoA hydratase, EchA5
F: Enoyl-CoA hydratase, EchA5


Theoretical massNumber of molelcules
Total (without water)161,9566
Polymers161,9566
Non-polymers00
Water12,106672
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23590 Å2
ΔGint-132 kcal/mol
Surface area45670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.040, 118.920, 132.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: 6 / Auth seq-ID: 4 - 214 / Label seq-ID: 9 - 219

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

#1: Protein
Enoyl-CoA hydratase, EchA5 /


Mass: 26992.637 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum M (bacteria) / Strain: ATCC BAA-535 / M / Gene: echA5, MMAR_1004 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HSK3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 672 / 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: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Crystal tracking ID 218457h19. JCSG+ screen condition H10: 0.2 M ammonium acetate, 0.1 M Bis-Tris propane, 25% PEG3350, 46.3 mg/mL MymaA.00386.a.A1 PS00820, pH 5.5, VAPOR DIFFUSION, SITTING ...Details: Crystal tracking ID 218457h19. JCSG+ screen condition H10: 0.2 M ammonium acetate, 0.1 M Bis-Tris propane, 25% PEG3350, 46.3 mg/mL MymaA.00386.a.A1 PS00820, pH 5.5, 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
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 23, 2011 / Details: VariMax
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: 75404 / Num. obs: 73428 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 31.017 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.08
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
2.15-2.212.60.4612.44129175531501490.7
2.21-2.270.4312.9513358489591.7
2.27-2.330.3323.7714304493794.1
2.33-2.40.2834.4314972486895.8
2.4-2.480.2495.1615719481497.6
2.48-2.570.2335.6916334471998.9
2.57-2.670.1976.8517115457399.5
2.67-2.780.1767.7818248443099.7
2.78-2.90.1549.5120350427099.9
2.9-3.040.13110.92204034065100
3.04-3.210.11112.6919685389799.7
3.21-3.40.09115.5818568367399.6
3.4-3.630.07817.9317517346299.6
3.63-3.930.06820.8515987319098.9
3.93-4.30.05823.714777296998.5
4.3-4.810.05325.4613161268698.5
4.81-5.550.05623.4111789238698.7
5.55-6.80.05721.910162206599.5
6.8-9.620.04926.757628159898.1
9.620.04628.73400991795.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 52.91 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å39.38 Å
Translation3 Å39.38 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 3H81

3h81


Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.192 / WRfactor Rwork: 0.1515 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8667 / SU B: 10.685 / SU ML: 0.124 / SU R Cruickshank DPI: 0.2451 / SU Rfree: 0.1878 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 3698 5 %RANDOM
Rwork0.1683 ---
obs0.1706 73236 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.02 Å2 / Biso mean: 24.4438 Å2 / Biso min: 3.99 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20 Å20 Å2
2--0.71 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10339 0 0 672 11011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02210535
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.96214356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86851446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.91223.302421
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.948151535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.45615100
X-RAY DIFFRACTIONr_chiral_restr0.0910.21668
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218139
X-RAY DIFFRACTIONr_mcbond_it0.631.57151
X-RAY DIFFRACTIONr_mcangle_it1.148211254
X-RAY DIFFRACTIONr_scbond_it2.10633384
X-RAY DIFFRACTIONr_scangle_it3.2994.53098
Refine LS restraints NCS

Ens-ID: 1 / Number: 1471 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.325
2BLOOSE POSITIONAL0.355
3CLOOSE POSITIONAL0.415
4DLOOSE POSITIONAL0.395
5ELOOSE POSITIONAL0.275
6FLOOSE POSITIONAL0.45
1ALOOSE THERMAL3.2210
2BLOOSE THERMAL2.9410
3CLOOSE THERMAL3.0810
4DLOOSE THERMAL2.9810
5ELOOSE THERMAL2.3510
6FLOOSE THERMAL2.2610
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 253 -
Rwork0.235 4739 -
all-4992 -
obs--90.47 %
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)
10.4309-0.12270.39380.183-0.28190.93070.029-0.019-0.0750.04630.0477-0.0215-0.0299-0.0839-0.07670.0590.0229-0.0110.05460.01520.0464-3.584-3.82673.4598
20.15710.13830.03861.4082-0.5890.7212-0.01440.0542-0.02110.2145-0.0811-0.1919-0.1825-0.01710.09550.12260.0155-0.0620.0599-0.00560.03987.888223.773-4.9422
30.3720.00670.0480.6167-0.02230.35460.01360.0526-0.0548-0.0176-0.01260.0263-0.0161-0.0295-0.0010.03370.02220.00120.0621-0.05580.07028.2036-2.348-41.0356
40.66320.07150.18970.3789-0.04730.42880.0229-0.0260.05940.0472-0.0157-0.019-0.02360.0423-0.00710.03730.00180.00670.0455-0.04590.067732.495910.3377-25.5658
50.55040.4177-0.0580.7714-0.09080.42240.0811-0.0389-0.07270.1437-0.08540.01580.09450.00690.00430.0907-0.006600.0141-0.01240.062320.9914-18.7405-17.0071
60.31670.00490.17850.6257-0.12050.61020.00170.0464-0.05320.00020.06240.0333-0.0822-0.1415-0.06410.02530.0510.00090.11940.00520.0318-13.645110.9867-22.9856
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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