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- PDB-4di1: Crystal structure of enoyl-CoA hydratase EchA17 from Mycobacteriu... -

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Basic information

Entry
Database: PDB / ID: 4di1
TitleCrystal structure of enoyl-CoA hydratase EchA17 from Mycobacterium marinum
ComponentsEnoyl-CoA hydratase EchA17
KeywordsLYASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / tuberculosis / ortholog / marine parasite / 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/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 EchA17
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 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 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: 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_ncs_dom_lim / 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_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 / _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 EchA17
B: Enoyl-CoA hydratase EchA17
C: Enoyl-CoA hydratase EchA17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4544
Polymers87,3923
Non-polymers621
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-57 kcal/mol
Surface area26610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.870, 87.500, 107.390
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
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA2 - 23523 - 256
21ALAALABB2 - 23523 - 256
12GLNGLNAA2 - 23823 - 259
22GLNGLNCC2 - 23823 - 259
13ALAALABB2 - 23523 - 256
23ALAALACC2 - 23523 - 256

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Enoyl-CoA hydratase EchA17


Mass: 29130.688 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: BAA-535/M / Gene: echA17, MMAR_1662 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HHI0
#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.: 348 / 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: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MymaA.00358.f.A1 at 47.5 mg/mL against PACT C10 focus screen, 0.2 M MgCl2, 30% PEG 6000, 0.1 M Hepes pH 7.5, 20% ethylene glycol as cryo-protectant, crystal tracking ID 219914f12, VAPOR ...Details: MymaA.00358.f.A1 at 47.5 mg/mL against PACT C10 focus screen, 0.2 M MgCl2, 30% PEG 6000, 0.1 M Hepes pH 7.5, 20% ethylene glycol as cryo-protectant, crystal tracking ID 219914f12, 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: May 22, 2011 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 35070 / Num. obs: 34771 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 27.718 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 12.14
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.25-2.310.5313.39110322537199.2
2.31-2.370.4743.87109432473199.2
2.37-2.440.44.49106362405199.3
2.44-2.520.3794.73104772351199.4
2.52-2.60.3265.47101652260199.4
2.6-2.690.3025.8899812212199.5
2.69-2.790.2816.1895542098199.5
2.79-2.90.2416.9695702078199.4
2.9-3.030.27.9590691962199.7
3.03-3.180.1589.6388481902199.6
3.18-3.350.12812.0783661807199.8
3.35-3.560.09316.9878201703199.5
3.56-3.80.07221.9273031606199.1
3.8-4.110.0626.3667601490199.3
4.11-4.50.05328.9763951399198.9
4.5-5.030.05228.4157291254199.1
5.03-5.810.07220.7951371118198.2
5.81-7.120.069214365953198.2
7.12-10.060.03140.143260739196.6
10.06-500.02349.411715424191.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å45.77 Å
Translation3 Å45.77 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDb entry 3H81

3h81


Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.1847 / WRfactor Rwork: 0.1525 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8553 / SU B: 11.191 / SU ML: 0.144 / SU R Cruickshank DPI: 0.3063 / SU Rfree: 0.2153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.306 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 1747 5 %RANDOM
Rwork0.1852 ---
obs0.1874 34770 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.75 Å2 / Biso mean: 20.5393 Å2 / Biso min: 4.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5177 0 4 348 5529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195312
X-RAY DIFFRACTIONr_bond_other_d0.0060.023484
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9697242
X-RAY DIFFRACTIONr_angle_other_deg1.30138443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5795722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3622.694219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75315779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4991554
X-RAY DIFFRACTIONr_chiral_restr0.0820.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216149
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021133
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: RESTRAINTS / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A73240.1
12B73240.1
21A72240.1
22C72240.1
31B72910.07
32C72910.07
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 116 -
Rwork0.248 2239 -
all-2355 -
obs--99.16 %
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)
10.0873-0.13210.18430.7298-0.0960.6004-0.0203-0.00250.01990.01540.0197-0.0096-0.05510.03620.00070.0061-0.0003-0.00530.03660.00220.0436-24.169167.158443.4966
20.2364-0.2131-0.2830.21430.24770.8817-0.0389-0.01450.00990.04790.01-0.01040.0740.08630.02880.03090.0183-0.00690.02950.00930.0224-18.783339.860924.5226
30.1282-0.1306-0.11170.62980.3740.4850.0265-0.00430.0114-0.11280.0171-0.0726-0.05990.0115-0.04360.04480.0150.02310.0184-0.00030.0209-24.702368.960610.5131
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 239
2X-RAY DIFFRACTION2B1 - 236
3X-RAY DIFFRACTION3C2 - 240

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