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- PDB-4fn8: Crystal structure of the Mtb enoyl CoA isomerase (Rv0632c)in comp... -

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Basic information

Entry
Database: PDB / ID: 4fn8
TitleCrystal structure of the Mtb enoyl CoA isomerase (Rv0632c)in complex with acetoacetyl 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
ACETOACETYL-COENZYME A / Enoyl-CoA hydratase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.831 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 (ECI)
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 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,6075
Polymers24,4671
Non-polymers1,1404
Water6,612367
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)76,82015
Polymers73,4013
Non-polymers3,41912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area9930 Å2
ΔGint-82 kcal/mol
Surface area24090 Å2
MethodPISA
2
A: Enoyl-CoA hydratase/isomerase family protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)153,64030
Polymers146,8026
Non-polymers6,83924
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_545x,x-y-1,-z+1/21
Buried area23810 Å2
ΔGint-294 kcal/mol
Surface area45330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.496, 75.496, 136.852
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-303-

SO4

21A-303-

SO4

31A-304-

SO4

41A-499-

HOH

51A-622-

HOH

61A-640-

HOH

71A-718-

HOH

81A-739-

HOH

91A-746-

HOH

101A-748-

HOH

111A-758-

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-CAA / ACETOACETYL-COENZYME A


Mass: 851.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H40N7O18P3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.6M ammonium sulfate, 0.1M MES 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 30, 2009 / Details: osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionRedundancy: 7.2 % / Av σ(I) over netI: 42.59 / Number: 151417 / Rmerge(I) obs: 0.06 / Χ2: 2.03 / D res high: 1.83 Å / D res low: 50 Å / Num. obs: 21089 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.975098.110.0261.4986.6
3.944.9710010.031.7387.2
3.443.9499.910.0352.0057.3
3.133.4410010.0412.0957.2
2.93.1310010.0522.2517.3
2.732.910010.0612.2177.3
2.62.7310010.072.1697.3
2.482.610010.0782.1367.2
2.392.4810010.0852.27.3
2.312.3910010.0942.1177.3
2.232.3110010.1032.357.2
2.172.2310010.1122.267.2
2.112.1710010.1252.1647.3
2.062.1199.710.1492.1487.2
2.012.0699.910.1672.0397.2
1.972.0199.910.1831.8827.2
1.931.9710010.2091.9237.2
1.91.9310010.2531.8597.1
1.861.910010.281.7587.1
1.831.8699.910.3311.7946.9
ReflectionResolution: 1.83→50 Å / Num. all: 21089 / Num. obs: 21089 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 17.87 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Χ2: 2.031 / Net I/σ(I): 17.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.83-1.866.90.33110251.794199.9
1.86-1.97.10.2810341.7581100
1.9-1.937.10.25310331.8591100
1.93-1.977.20.20910141.9231100
1.97-2.017.20.18310311.882199.9
2.01-2.067.20.16710232.039199.9
2.06-2.117.20.14910442.148199.7
2.11-2.177.30.12510262.1641100
2.17-2.237.20.11210372.261100
2.23-2.317.20.10310432.351100
2.31-2.397.30.09410322.1171100
2.39-2.487.30.08510432.21100
2.48-2.67.20.07810552.1361100
2.6-2.737.30.0710492.1691100
2.73-2.97.30.06110752.2171100
2.9-3.137.30.05210532.2511100
3.13-3.447.20.04110792.0951100
3.44-3.947.30.03510812.005199.9
3.94-4.977.20.0311121.7381100
4.97-506.60.02612001.498198.1

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4fn7


Resolution: 1.831→25.35 Å / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.9014 / SU ML: 0.18 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 15.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1888 1079 5.13 %random
Rwork0.1494 ---
all0.1514 21038 --
obs0.1514 21038 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.986 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso max: 71.6 Å2 / Biso mean: 18.8567 Å2 / Biso min: 5.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.1072 Å20 Å2-0 Å2
2--0.1072 Å2-0 Å2
3----0.2143 Å2
Refinement stepCycle: LAST / Resolution: 1.831→25.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1681 0 69 367 2117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071809
X-RAY DIFFRACTIONf_angle_d1.0472473
X-RAY DIFFRACTIONf_chiral_restr0.067280
X-RAY DIFFRACTIONf_plane_restr0.007317
X-RAY DIFFRACTIONf_dihedral_angle_d18.734688
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8306-1.91390.22071390.153224132552
1.9139-2.01470.20691360.143424412577
2.0147-2.14090.19281450.140124332578
2.1409-2.30610.15121290.132324552584
2.3061-2.5380.20611350.140624552590
2.538-2.90480.19261400.148325112651
2.9048-3.6580.1811240.142725312655
3.658-25.35250.16821310.15827202851

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