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- PDB-3qk8: Crystal structure of enoyl-coA hydratase EchA15 from Mycobacteriu... -

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Basic information

Entry
Database: PDB / ID: 3qk8
TitleCrystal structure of enoyl-coA hydratase EchA15 from Mycobacterium marinum in complex with an unknown ligand
ComponentsEnoyl-CoA hydratase EchA15
KeywordsLYASE / SSGCID / NIH / NIAID / SBRI / UW / Emerald BioStructures / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


enoyl-CoA hydratase activity
Similarity search - Function
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, 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 ...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, 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 / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Enoyl-CoA hydratase EchA15
Similarity search - Component
Biological speciesMycobacterium marinum M (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.6 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 ...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 EchA15
B: Enoyl-CoA hydratase EchA15
C: Enoyl-CoA hydratase EchA15
D: Enoyl-CoA hydratase EchA15
E: Enoyl-CoA hydratase EchA15
F: Enoyl-CoA hydratase EchA15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,73128
Polymers176,7036
Non-polymers1,02922
Water23,2751292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28620 Å2
ΔGint-80 kcal/mol
Surface area43950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.990, 129.530, 78.610
Angle α, β, γ (deg.)90.000, 108.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Enoyl-CoA hydratase EchA15


Mass: 29450.467 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: echA15, MMAR_2037 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2HM22
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 5 / Source method: obtained synthetically
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1292 / 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: 2.03 Å3/Da / Density % sol: 39.36 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Internal tracking number 218997A9. JCSG screen condition A9: 20% PEG3350, 0.2 M ammonium chloride. MymaA.00829.b.A1 PS00862 at 43.78mg/ml., pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.6→48.883 Å / Num. all: 184428 / Num. obs: 181397 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5256 % / Biso Wilson estimate: 21.199 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 23.92
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
1.6-1.643.6710.314444391136291209288.7
1.64-1.690.2834.9550111296598.2
1.69-1.740.2396.3587891270798.5
1.74-1.790.2027.4572521237598.6
1.79-1.850.169.2556221200198.7
1.85-1.910.12911.4538651164098.9
1.91-1.980.10214.1517761118299.1
1.98-2.070.08217.5503591087399.1
2.07-2.160.06920.7479701035599.2
2.16-2.260.05525.246112997399.4
2.26-2.390.04629.543904947299.4
2.39-2.530.04132.841609898699.5
2.53-2.70.03835.438959843099.6
2.7-2.920.03439.836129785999.8
2.92-3.20.02846.133319727099.8
3.2-3.580.02355.329946658499.7
3.58-4.130.01963.926061580299.9
4.13-5.060.01668.922271490099.8
5.06-7.160.01863.817907382699.7
7.160.01377.79682210598.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.88 Å
Translation2.5 Å48.88 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 1WZ8

1wz8


Resolution: 1.6→48.883 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.604 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.164 9122 5 %RANDOM
Rwork0.137 ---
all0.138 184428 --
obs0.138 181313 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.753 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.15 Å2
2--0.36 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11683 0 109 1292 13084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02212412
X-RAY DIFFRACTIONr_bond_other_d0.0010.028349
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.97216935
X-RAY DIFFRACTIONr_angle_other_deg1.136320304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8451653
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66523.087541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.828151955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.615113
X-RAY DIFFRACTIONr_chiral_restr0.1040.21934
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02114139
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022591
X-RAY DIFFRACTIONr_mcbond_it0.9061.57876
X-RAY DIFFRACTIONr_mcbond_other0.291.53231
X-RAY DIFFRACTIONr_mcangle_it1.518212633
X-RAY DIFFRACTIONr_scbond_it2.50834536
X-RAY DIFFRACTIONr_scangle_it4.0144.54249
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 644 -
Rwork0.226 11430 -
all-12074 -
obs-12092 88.76 %
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)
10.1304-0.0666-0.08410.3697-0.02030.3683-0.01220.0544-0.0061-0.0526-0.0051-0.03120.03980.01570.01740.01870.00170.01540.04270.00640.016362.57820.978-0.358
20.2224-0.023-0.05280.3416-0.00980.4922-0.01250.01140.0726-0.0168-0.00130.0173-0.0865-0.02480.01380.02320.0108-0.01110.01910.00780.032239.71650.33313.776
30.2477-0.02020.08360.3148-0.07080.4033-0.00760.0718-0.026-0.0316-0.01710.01940.0782-0.08080.02480.0208-0.02450.00350.0552-0.01910.016129.23517.776.192
40.33310.0317-0.00620.40040.10190.6011-0.0563-0.058-0.06280.0607-0.0173-0.020.14530.03050.07350.06180.02150.02560.01940.02380.03858.6147.61331.201
50.37440.1431-0.01210.26510.03390.38450.0048-0.0612-0.01410.039-0.01720.00530.0055-0.06260.01250.0105-0.00010.00440.0427-0.00250.003632.52128.34739.087
60.66390.0794-0.26410.142-0.01160.44430.0304-0.04760.11470.02530.0146-0.0282-0.03310.0644-0.04510.0087-0.0041-0.00750.023-0.00690.047768.96740.36427.639
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 270
2X-RAY DIFFRACTION2B-3 - 270
3X-RAY DIFFRACTION3C-3 - 270
4X-RAY DIFFRACTION4D-3 - 270
5X-RAY DIFFRACTION5E-3 - 270
6X-RAY DIFFRACTION6F-3 - 270

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