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- PDB-3r9q: Structure of a probable enoyl-coa hydratase/isomerase from Mycoba... -

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Basic information

Entry
Database: PDB / ID: 3r9q
TitleStructure of a probable enoyl-coa hydratase/isomerase from Mycobacterium abscessus ATCC 19977 / DSM 44196
Componentsenoyl-coA hydratase/isomerase
KeywordsLYASE / ISOMERASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease / enoyl-coa hydratase/isomerase
Function / homology
Function and homology information


enoyl-CoA hydratase activity / isomerase 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
Probable enoyl-coa hydratase/isomerase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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
DepositionMar 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
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/isomerase
B: enoyl-coA hydratase/isomerase
C: enoyl-coA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2376
Polymers82,0743
Non-polymers1633
Water12,989721
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10330 Å2
ΔGint-78 kcal/mol
Surface area25050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.318, 98.213, 103.951
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein enoyl-coA hydratase/isomerase


Mass: 27357.959 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / DSM 44196 / Gene: MAB_3857c / Production host: Escherichia coli (E. coli)
References: UniProt: B1MGI6, enoyl-CoA hydratase, Delta3-Delta2-enoyl-CoA isomerase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 3.06 Å3/Da / Density % sol: 59.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M ammonium chloride, 20% PEG6000, 0.1 M HEPES, pH 7.0, cryoprotectant: 25% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 10, 2011
RadiationMonochromator: asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 58642 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.099 / Χ2: 1.02 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.146.40.40228750.992199.4
2.14-2.186.40.35528871.034199.4
2.18-2.226.50.35328771.052199.2
2.22-2.266.30.38628831.062199.1
2.26-2.316.50.31328941.075199.3
2.31-2.376.50.23428801.039199.3
2.37-2.426.60.21828831.058199.1
2.42-2.496.60.20828841.076199.3
2.49-2.566.60.19228921.056199.3
2.56-2.656.60.16629370.979199.6
2.65-2.746.60.15629121.059199.6
2.74-2.856.70.13629050.974199.8
2.85-2.986.70.11329410.974199.9
2.98-3.146.70.10829240.958199.9
3.14-3.336.70.09729480.954199.9
3.33-3.596.60.08429621.003199.9
3.59-3.956.50.07629731.052199.9
3.95-4.526.50.05829721.0131100
4.52-5.76.70.04630380.9581100
5.7-506.60.03131751.043199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.73 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.11 Å
Translation2.5 Å49.11 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QKA

3qka


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.1876 / WRfactor Rwork: 0.1587 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8912 / SU B: 6.99 / SU ML: 0.084 / SU R Cruickshank DPI: 0.1511 / SU Rfree: 0.1346 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 2964 5.1 %RANDOM
Rwork0.1608 ---
obs0.1623 58337 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.16 Å2 / Biso mean: 22.989 Å2 / Biso min: 5.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5241 0 8 721 5970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225378
X-RAY DIFFRACTIONr_bond_other_d0.0070.023579
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.9577336
X-RAY DIFFRACTIONr_angle_other_deg0.95638687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3155722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03123.117231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02315798
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4111555
X-RAY DIFFRACTIONr_chiral_restr0.080.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216205
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021086
X-RAY DIFFRACTIONr_mcbond_it0.631.53556
X-RAY DIFFRACTIONr_mcbond_other0.1361.51463
X-RAY DIFFRACTIONr_mcangle_it1.19325646
X-RAY DIFFRACTIONr_scbond_it2.10131822
X-RAY DIFFRACTIONr_scangle_it3.3414.51685
LS refinement shellResolution: 2.104→2.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 191 -
Rwork0.176 3829 -
all-4020 -
obs--93.25 %
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)
10.2-0.0946-0.02790.4614-0.25550.21730.0078-0.00110.02090.040.03410.0684-0.0393-0.0071-0.04180.0082-0.00090.00980.01020.00720.037927.705552.0535-7.7808
20.3909-0.0239-0.1560.2038-0.03560.3412-0.0144-0.0637-0.03010.02480.00370.01520.00910.01580.01070.00680.00070.00160.01660.01110.012144.31526.93833.6172
30.2511-0.0727-0.01690.4225-0.07640.21430.01690.0281-0.0007-0.0474-0.0122-0.0350.0040.0185-0.00480.0127-0.00310.00690.0144-0.00010.006752.740941.785-23.7535
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 238
2X-RAY DIFFRACTION2B6 - 245
3X-RAY DIFFRACTION3C6 - 247

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