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- PDB-4f47: The Structure of Enoyl-CoA hydratase EchA19 from Mycobacterium marinum -

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Basic information

Entry
Database: PDB / ID: 4f47
TitleThe Structure of Enoyl-CoA hydratase EchA19 from Mycobacterium marinum
ComponentsEnoyl-CoA hydratase EchA19
KeywordsLYASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease / NIAID / National Institute of Allergy and Infectious Diseases
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 EchA19
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle 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
DepositionMay 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 EchA19


Theoretical massNumber of molelcules
Total (without water)29,8021
Polymers29,8021
Non-polymers00
Water4,053225
1
A: Enoyl-CoA hydratase EchA19

A: Enoyl-CoA hydratase EchA19

A: Enoyl-CoA hydratase EchA19


Theoretical massNumber of molelcules
Total (without water)89,4063
Polymers89,4063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area10060 Å2
ΔGint-71 kcal/mol
Surface area25620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.440, 76.440, 73.490
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-330-

HOH

21A-489-

HOH

31A-493-

HOH

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Components

#1: Protein Enoyl-CoA hydratase EchA19


Mass: 29802.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535 / M / Gene: echA19, MMAR_5002 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HI06
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.08 Å3/Da / Density % sol: 40.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20mg/ml MymaA.01530.e.A1, 200mM potassium citrate, 20% PEG 3350, cryoprotection 20% ethylene glycol, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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: May 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 25435 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.522 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.75-1.80.2683.646698184199
1.8-1.840.2554.2274871797100
1.84-1.90.2234.997606175899.9
1.9-1.960.1855.9677551716100
1.96-2.020.1477.1978541666100
2.02-2.090.1348.5878651592100
2.09-2.170.11710.058289157699.9
2.17-2.260.12111.7494791503100
2.26-2.360.11512.829776144199.9
2.36-2.470.10314.6310065138299.8
2.47-2.610.10815.1910174129799.8
2.61-2.770.10216.6410591123599.8
2.77-2.960.10119.14120601194100
2.96-3.20.09521.43113411100100
3.2-3.50.0923.1210260100199.9
3.5-3.910.08224.94922692499.5
3.91-4.520.08526.09792381398.9
4.52-5.530.08425.4670070499.7
5.53-7.830.08225.115326558100
7.830.06925.46297933798.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RSI

3rsi


Resolution: 1.75→38.22 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.2071 / WRfactor Rwork: 0.1749 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8904 / SU B: 3.699 / SU ML: 0.064 / SU R Cruickshank DPI: 0.1107 / SU Rfree: 0.1065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2063 1295 5.1 %RANDOM
Rwork0.1747 ---
obs0.1763 25435 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 48.26 Å2 / Biso mean: 16.9398 Å2 / Biso min: 7.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å2-0.46 Å20 Å2
2---0.92 Å20 Å2
3---1.39 Å2
Refinement stepCycle: LAST / Resolution: 1.75→38.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 0 225 2003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191832
X-RAY DIFFRACTIONr_bond_other_d0.0010.021263
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9762483
X-RAY DIFFRACTIONr_angle_other_deg0.92233079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9435242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.57123.275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57515315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8871518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212060
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02362
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 91 -
Rwork0.185 1623 -
all-1714 -
obs--98.9 %
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)
11.0534-0.298-0.21991.13890.05980.84280.00070.016-0.20830.014-0.03090.02980.07210.00970.03020.0460.01160.00140.0255-0.00340.080111.363120.255520.8007
20.66540.06740.1010.4175-0.02690.10960.0110.0805-0.0517-0.0274-0.0117-0.01660.03640.00670.00070.05880.00450.00770.0676-0.00420.02844.398233.551118.4216
33.3918-0.0694-1.59271.15940.36511.9175-0.04910.0103-0.02570.0292-0.0045-0.0891-0.08510.07380.05370.0183-0.0011-0.01980.07090.01210.05131.637841.281922.9981
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 126
2X-RAY DIFFRACTION2A127 - 244
3X-RAY DIFFRACTION3A245 - 274

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