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- PDB-3trr: Crystal structure of a probable enoyl-CoA hydratase/isomerase fro... -

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Basic information

Entry
Database: PDB / ID: 3trr
TitleCrystal structure of a probable enoyl-CoA hydratase/isomerase from Mycobacterium abscessus
ComponentsProbable enoyl-CoA hydratase/isomerase
KeywordsISOMERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


enoyl-CoA hydratase activity / isomerase 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
DI(HYDROXYETHYL)ETHER / Probable enoyl-CoA hydratase/isomerase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: 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_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: Probable enoyl-CoA hydratase/isomerase
B: Probable enoyl-CoA hydratase/isomerase
C: Probable enoyl-CoA hydratase/isomerase
D: Probable enoyl-CoA hydratase/isomerase
E: Probable enoyl-CoA hydratase/isomerase
F: Probable enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,26311
Polymers159,8496
Non-polymers4145
Water8,917495
1
A: Probable enoyl-CoA hydratase/isomerase
B: Probable enoyl-CoA hydratase/isomerase
C: Probable enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1416
Polymers79,9243
Non-polymers2163
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
ΔGint-56 kcal/mol
Surface area28680 Å2
MethodPISA
2
D: Probable enoyl-CoA hydratase/isomerase
E: Probable enoyl-CoA hydratase/isomerase
F: Probable enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1235
Polymers79,9243
Non-polymers1982
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-63 kcal/mol
Surface area27520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.427, 82.738, 157.163
Angle α, β, γ (deg.)90.00, 98.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Probable enoyl-CoA hydratase/isomerase


Mass: 26641.469 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / Gene: MAB_4588c / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1ML12
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 7.5
Details: INTERNAL TRACKING NUMBER219728. MORPHEUS SCREEN A5. 0.1M SODIUM HEPES; MOPS (ACID), 0.06M MGCL2/CACL2, 30% W/V PEGMME 550/ PEG 20,000, CRYO 20% ETHYLENE GLYCOL MYABA.01530.F.A1 PW30398 27. ...Details: INTERNAL TRACKING NUMBER219728. MORPHEUS SCREEN A5. 0.1M SODIUM HEPES; MOPS (ACID), 0.06M MGCL2/CACL2, 30% W/V PEGMME 550/ PEG 20,000, CRYO 20% ETHYLENE GLYCOL MYABA.01530.F.A1 PW30398 27.53MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2011
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.09→46.56 Å / Num. obs: 95231 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 37.761 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 14.98

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QXI

3qxi


Resolution: 2.09→46.56 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.84 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 4760 5 %RANDOM
Rwork0.191 ---
all0.193 ---
obs0.193 95189 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å2-0.03 Å2
2---2.68 Å20 Å2
3---2.12 Å2
Refinement stepCycle: LAST / Resolution: 2.09→46.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10804 0 27 495 11326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911024
X-RAY DIFFRACTIONr_bond_other_d0.0010.027183
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.97615007
X-RAY DIFFRACTIONr_angle_other_deg1.047317588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82251515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90924.594431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.258151656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9591576
X-RAY DIFFRACTIONr_chiral_restr0.0740.21782
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112736
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022152
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 341 -
Rwork0.216 5899 -
obs--89.48 %
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)
10.68450.30130.06931.1201-0.14860.5984-0.002-0.1164-0.02220.07060.0169-0.03550.18620.0455-0.01490.11870.0027-0.020.06580.02180.018913.7211-0.9683-51.8302
20.51220.19880.29761.36650.01850.92270.1129-0.0543-0.02070.1034-0.09370.18560.0206-0.1634-0.01920.0299-0.00860.00920.09910.00040.17-10.870211.9718-69.4395
30.7042-0.06510.32031.2052-0.23860.61250.0023-0.01840.13960.0151-0.0215-0.1366-0.01940.06680.01920.0178-0.01520.00010.03280.00530.073516.698428.6314-65.0707
40.49310.0655-0.06621.2175-0.37851.34440.03470.03860.0446-0.0430.01650.2981-0.035-0.2904-0.05120.020.0012-0.04070.1810.00630.1455-20.111140.3888-9.1485
51.32450.4828-0.56910.5567-0.06970.7781-0.05620.0257-0.1364-0.09340.0477-0.09090.13130.04410.00860.11250.0075-0.02350.0933-0.00660.03416.940424.0888-15.4406
60.67430.05830.04371.2790.05220.89080.03090.08050.0902-0.20280.0765-0.0648-0.1164-0.0096-0.10730.1349-0.0160.01940.0880.02820.03554.65355.4828-23.6167
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 252
2X-RAY DIFFRACTION2B3 - 252
3X-RAY DIFFRACTION3C1 - 252
4X-RAY DIFFRACTION4D3 - 252
5X-RAY DIFFRACTION5E2 - 252
6X-RAY DIFFRACTION6F2 - 252

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