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- PDB-3qmj: Crystal structure of Enoyl-CoA hydratase EchA8_6 from Mycobacteri... -

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Basic information

Entry
Database: PDB / ID: 3qmj
TitleCrystal structure of Enoyl-CoA hydratase EchA8_6 from Mycobacterium marinum
ComponentsEnoyl-CoA hydratase, EchA8_6
KeywordsLYASE / SSGCID / NIH / NIAID / SBRI / UW / Emerald BioStructures / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


delta(3)-delta(2)-enoyl-CoA isomerase activity / peroxisome
Similarity search - Function
: / 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 / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Enoyl-CoA hydratase, EchA8_6
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2.2 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
DepositionFeb 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Sep 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, EchA8_6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3853
Polymers27,2931
Non-polymers922
Water2,000111
1
A: Enoyl-CoA hydratase, EchA8_6
hetero molecules

A: Enoyl-CoA hydratase, EchA8_6
hetero molecules

A: Enoyl-CoA hydratase, EchA8_6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1569
Polymers81,8803
Non-polymers2766
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area7260 Å2
ΔGint-40 kcal/mol
Surface area24120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.820, 115.820, 115.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Enoyl-CoA hydratase, EchA8_6


Mass: 27293.178 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: echA8_6, MMAR_2759 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2HD64
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.41 Å3/Da / Density % sol: 48.906 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: Internal tracking number 218458A5. JCSG screen condition A5: 20% PEG3350, 0.2 M Magnesium formate. MymaA.00358.c.A1 PS00818 at 69.82 mg/ml., pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→33.43 Å / Num. all: 13294 / Num. obs: 13222 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 37.348 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 23.62
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
2.2-2.267.10.4615.8670397294096.7
2.26-2.320.524.7708193097.3
2.32-2.390.3776.1706890599.9
2.39-2.460.3137.2701889699.9
2.46-2.540.287.76884878100
2.54-2.630.23196656846100
2.63-2.730.229.8627680399.9
2.73-2.840.16711.5612877599.5
2.84-2.970.1313.76110769100
2.97-3.110.10515.8562671099.9
3.11-3.280.08120.45399682100
3.28-3.480.06130.15083643100
3.48-3.720.0540.24855626100
3.72-4.020.03853.9433056399.3
4.02-4.40.02664.74127523100
4.4-4.920.02568.73744477100
4.92-5.680.03155.23362432100
5.68-6.960.03350.52843366100
6.96-9.840.0281.22187288100
9.840.01698114917097.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å36.63 Å
Translation2.5 Å36.63 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 3FDU

3fdu


Resolution: 2.2→33.43 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.287 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.217 650 4.9 %RANDOM
Rwork0.183 ---
obs0.185 13166 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.051 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1542 0 6 111 1659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221573
X-RAY DIFFRACTIONr_bond_other_d0.0010.021030
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.9832139
X-RAY DIFFRACTIONr_angle_other_deg0.95532521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0585209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50523.68457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.39615242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2921511
X-RAY DIFFRACTIONr_chiral_restr0.0780.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211764
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02304
X-RAY DIFFRACTIONr_mcbond_it0.691.51054
X-RAY DIFFRACTIONr_mcbond_other0.141.5426
X-RAY DIFFRACTIONr_mcangle_it1.29521662
X-RAY DIFFRACTIONr_scbond_it2.0223519
X-RAY DIFFRACTIONr_scangle_it3.3244.5477
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 38 -
Rwork0.301 879 -
all-917 -
obs--96.32 %
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)
10.8136-0.21270.24020.78861.01533.79780.0265-0.132-0.07410.1108-0.11730.0674-0.1435-0.42760.09090.19540.05820.03840.1827-0.00310.087118.169-10.566-13.7
21.9367-0.89081.30682.78690.06991.25250.0901-0.0423-0.19260.15160.02350.02350.0579-0.0454-0.11370.17790.02610.00750.1553-0.02060.118731.436-21.91-20.117
35.78883.24190.81452.68951.15553.7525-0.22070.0341-0.0417-0.1797-0.1610.1141-0.2525-0.5470.38170.12460.09590.02730.1961-0.07110.091714.211-14.746-30.434
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 132
2X-RAY DIFFRACTION2A133 - 179
3X-RAY DIFFRACTION3A180 - 252

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