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- PDB-4fnb: Crystal structure of the Mtb enoyl CoA isomerase (Rv0632c) in com... -

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Basic information

Entry
Database: PDB / ID: 4fnb
TitleCrystal structure of the Mtb enoyl CoA isomerase (Rv0632c) in complex with hydroxybutyrl CoA
ComponentsEnoyl-CoA hydratase/isomerase family protein
KeywordsISOMERASE / Structural Genomics / TB Structural Genomics Consortium / TBSGC / crotonase superfamily
Function / homology
Function and homology information


enoyl-CoA hydratase / enoyl-CoA hydratase activity / fatty acid beta-oxidation / plasma membrane / cytosol
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
3-HYDROXYBUTANOYL-COENZYME A / Enoyl-CoA hydratase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsBruning, J.B. / Gao, N. / Hernandez, E.D. / Li, H. / Dang, N. / Hung, L.W. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: Crystal Structure and Mechanism of the Prokaryotic Enoyl CoA Isomerase
Authors: Bruning, J.B. / Gao, N. / Hernandez, E.D. / Li, H. / Dang, N. / Hung, L.W. / Moran, S. / Sacchettini, J.C.
History
DepositionJun 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6095
Polymers24,4671
Non-polymers1,1424
Water4,197233
1
A: Enoyl-CoA hydratase/isomerase family protein
hetero molecules

A: Enoyl-CoA hydratase/isomerase family protein
hetero molecules

A: Enoyl-CoA hydratase/isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,82615
Polymers73,4013
Non-polymers3,42512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7200 Å2
ΔGint-106 kcal/mol
Surface area27450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.136, 70.136, 151.557
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-303-

SO4

21A-303-

SO4

31A-304-

SO4

41A-539-

HOH

51A-575-

HOH

61A-609-

HOH

71A-617-

HOH

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Components

#1: Protein Enoyl-CoA hydratase/isomerase family protein / Enoyl-coA hydratase homolog / PROBABLE ENOYL-CoA HYDRATASE ECHA3 (ENOYL HYDRASE) (UNSATURATED ACYL- ...Enoyl-coA hydratase homolog / PROBABLE ENOYL-CoA HYDRATASE ECHA3 (ENOYL HYDRASE) (UNSATURATED ACYL-CoA HYDRATASE) (CROTONASE)


Mass: 24466.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: echA3, MT0660, Rv0632c / Plasmid: pvp16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P96907, enoyl-CoA hydratase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-3HC / 3-HYDROXYBUTANOYL-COENZYME A / 3-HYDROXYBUTYRYL-COENZYME A


Mass: 853.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H42N7O18P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 44.07 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 8, 2008 / Details: mirrors
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 5.96 % / Number: 125417 / Rmerge(I) obs: 0.062 / Χ2: 0.92 / D res high: 1.8 Å / D res low: 35.07 Å / Num. obs: 20872 / % possible obs: 98.3
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
3.8835.07990.0330.696.86189
3.083.881000.0430.717.246
2.693.081000.0630.79767
2.442.691000.0880.886.9673
2.272.4499.90.1150.956.89126
2.132.2799.70.1461.046.82168
2.032.1399.50.2011.176.88169
1.942.0399.20.2481.164.7781
1.861.9496.60.2991.163.218
1.81.8688.20.3511.172.245
ReflectionResolution: 1.8→35.07 Å / Num. all: 20872 / Num. obs: 20872 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.96 % / Biso Wilson estimate: 20.98 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 14
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.8-1.862.240.3512.2188.2
1.86-1.943.20.2993.1196.6
1.94-2.034.770.2484.2199.2
2.03-2.136.880.2016.1199.5
2.13-2.276.820.1468.1199.7
2.27-2.446.890.1159.6199.9
2.44-2.696.960.08812.41100
2.69-3.0870.06317.21100
3.08-3.887.20.04325.21100
3.88-35.076.860.03331.1199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK9.9Ldata reduction
PHASERphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FN7 subunit A

4fn7


Resolution: 1.8→35.07 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 0.22 / Isotropic thermal model: isotropic / σ(F): 0 / Phase error: 20.64 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.219 1077 5.17 %
Rwork0.187 --
obs0.189 20850 98.2 %
all-20850 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.7 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso mean: 21.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.9704 Å2-0 Å20 Å2
2---0.9704 Å20 Å2
3---1.9409 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1710 0 69 233 2012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071810
X-RAY DIFFRACTIONf_angle_d1.052461
X-RAY DIFFRACTIONf_dihedral_angle_d16.533685
X-RAY DIFFRACTIONf_chiral_restr0.07281
X-RAY DIFFRACTIONf_plane_restr0.016313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.88190.30321200.25042179X-RAY DIFFRACTION90
1.8819-1.98110.25361280.20362409X-RAY DIFFRACTION98
1.9811-2.10530.21321400.18752446X-RAY DIFFRACTION99
2.1053-2.26780.25791240.17332480X-RAY DIFFRACTION100
2.2678-2.49590.22361630.1682460X-RAY DIFFRACTION100
2.4959-2.8570.19621440.17162502X-RAY DIFFRACTION100
2.857-3.59890.19361230.16072572X-RAY DIFFRACTION100
3.5989-35.07480.19971350.1892725X-RAY DIFFRACTION99
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)
10.0324-0.11630.0230.78-0.02850.24650.00980.0445-0.02190.0060.00190.2846-0.0248-0.138-0.00880.11640.0008-00.1670.00730.2047-31.80272.479820.0045
20.1862-0.04660.06720.08-0.09470.1816-0.00950.0272-0.072-0.07630.05190.04360.0796-0.0194-0.06460.1768-0.0381-0.00480.1441-0.00490.1565-26.5318-10.903216.1126
30.08350.07130.01060.3319-0.23420.2208-0.01660.0052-0.01530.04390.0111-0.0427-0.04910.02170.00330.11650.0017-0.00360.1184-0.00610.1145-13.859-4.73420.5254
40.45910.08220.08710.24960.00570.02240.0811-0.1368-0.01490.0914-0.05920.0549-0.0155-0.06060.00460.1643-0.0050.01040.1428-0.02430.0827-20.81796.861433.7254
50.4004-0.00280.16180.0256-0.04030.1265-0.04510.01820.14170.01040.0456-0.0074-0.0904-0.00220.04360.15370.0108-0.01820.1584-0.00440.1537-14.723314.992415.3554
60.272-0.01790.01690.8382-0.08870.01890.04540.2798-0.0233-0.4017-0.0371-0.1491-0.0119-0.10460.02020.21490.01640.01180.2173-0.03250.1089-15.7573-6.77823.6374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 0:48)
2X-RAY DIFFRACTION2(chain A and resid 49:81)
3X-RAY DIFFRACTION3(chain A and resid 82:177)
4X-RAY DIFFRACTION4(chain A and resid 178:193)
5X-RAY DIFFRACTION5(chain A and resid 194:211)
6X-RAY DIFFRACTION6(chain A and resid 212:231)

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