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- PDB-3rsi: The structure of a putative enoyl-CoA hydratase/isomerase from My... -

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Basic information

Entry
Database: PDB / ID: 3rsi
TitleThe structure of a putative enoyl-CoA hydratase/isomerase from Mycobacterium abscessus ATCC 19977 / DSM 44196
ComponentsPutative enoyl-CoA hydratase/isomerase
KeywordsISOMERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


GMP Synthetase; Chain A, domain 3 - #220 / 2-enoyl-CoA Hydratase; Chain A, domain 1 - #20 / 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 / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / GMP Synthetase; Chain A, domain 3 ...GMP Synthetase; Chain A, domain 3 - #220 / 2-enoyl-CoA Hydratase; Chain A, domain 1 - #20 / 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 / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / GMP Synthetase; Chain A, domain 3 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Putative enoyl-CoA hydratase/isomerase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 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
DepositionMay 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 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: Putative enoyl-CoA hydratase/isomerase
B: Putative enoyl-CoA hydratase/isomerase
C: Putative enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,06129
Polymers84,7963
Non-polymers3,26526
Water9,386521
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19390 Å2
ΔGint-103 kcal/mol
Surface area25770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.850, 121.670, 64.550
Angle α, β, γ (deg.)90.000, 96.650, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative enoyl-CoA hydratase/isomerase


Mass: 28265.354 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_0836c / Production host: Escherichia coli (E. coli) / References: UniProt: B1MIA8
#2: 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
#3: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 20% PEG8000, 0.1M CHES pH9.5. Cryo protected with 25% ethylene glycol, 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: Jan 23, 2011
RadiationMonochromator: Varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→64.12 Å / Num. obs: 47423 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.605 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 18.07
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.050.1745.92139675441176
2.05-2.110.1726.87172316219189.3
2.11-2.170.1598.46230666707198.5
2.17-2.240.1569.13241166433198.4
2.24-2.310.13111.3230366287198.5
2.31-2.390.11711.69233526157199.4
2.39-2.480.10812.44225005919199.2
2.48-2.580.09713.66214825644199.4
2.58-2.70.08914.75209015501199.7
2.7-2.830.07616.76200555236199.7
2.83-2.980.06718.291898449481100
2.98-3.160.05520.861839347721100
3.16-3.380.04525.35171314435199.9
3.38-3.650.03831.21573941231100
3.65-40.03435.69144213811199.8
4-4.470.02642.4131943405199.9
4.47-5.160.02740.191172230181100
5.16-6.320.03729.8994225641100
6.32-8.940.02838.1175611970199.7
8.94-64.120.02152.2838891056197

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.42 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.97 Å
Translation2.5 Å19.97 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R9T

3r9t


Resolution: 2→19.97 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.1864 / WRfactor Rwork: 0.1448 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9052 / SU B: 6.926 / SU ML: 0.089 / SU R Cruickshank DPI: 0.1657 / SU Rfree: 0.1477 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 2371 5 %RANDOM
Rwork0.1497 ---
obs0.1521 46990 95.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 271.82 Å2 / Biso mean: 17.9431 Å2 / Biso min: 4.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å2-0.03 Å2
2--1.36 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 2→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5377 0 31 521 5929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215490
X-RAY DIFFRACTIONr_bond_other_d0.0010.023703
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.977450
X-RAY DIFFRACTIONr_angle_other_deg0.90438990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5975728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.83822.556223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20115882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0791558
X-RAY DIFFRACTIONr_chiral_restr0.0780.2868
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216228
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021108
X-RAY DIFFRACTIONr_mcbond_it0.6041.53609
X-RAY DIFFRACTIONr_mcbond_other0.151.51493
X-RAY DIFFRACTIONr_mcangle_it1.09925730
X-RAY DIFFRACTIONr_scbond_it1.87631881
X-RAY DIFFRACTIONr_scangle_it3.1764.51717
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 156 -
Rwork0.143 3073 -
all-3229 -
obs--89.77 %
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)
10.495-0.00350.01110.29660.140.3212-0.0076-0.10180.04840.0274-0.0136-0.00290.0319-0.00020.02120.009-0.00120.00210.0269-0.010.00717.709951.66610.5258
20.2887-0.0523-0.02420.21710.01390.3779-0.0053-0.01020.0394-0.03840.00480.01190.0179-0.02830.00050.0124-0.0051-0.00160.0053-0.00340.00888.860852.1252-16.7598
30.3138-0.07170.02580.2527-0.02470.19750.0010.0121-0.0058-0.0383-0.01320.01010.029-0.01240.01220.0106-0.00130.0010.0031-0.00220.001713.264948.3487-12.8186
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 261
2X-RAY DIFFRACTION2B4 - 261
3X-RAY DIFFRACTION3C4 - 261

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