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- PDB-4hc8: CRYSTAL STRUCTURE OF PROBABLE ENOYL-CoA HYDRATASE ECHA3 (Rv0632c,... -

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Basic information

Entry
Database: PDB / ID: 4hc8
TitleCRYSTAL STRUCTURE OF PROBABLE ENOYL-CoA HYDRATASE ECHA3 (Rv0632c, NYSGRC-019494) from Mycobacterium Tuberculosis H37Rv
ComponentsEnoyl-CoA hydratase/isomerase family protein
KeywordsLYASE / ECHA3 / UNSATURATED ACYL-CoA HYDRATASE / CROTONASE / Structural genomics / NYSGRC / PSI / New York Structural Genomics Research Consortium / PSI-Biology
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
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å
AuthorsSampathkumar, P. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of probable enoyl-CoA hydratase ECHA3 (Rv0632c, NYSGRC-019494) from Mycobacterium Tuberculosis H37Rv
Authors: Sampathkumar, P. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Gizzi, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / ...Authors: Sampathkumar, P. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Gizzi, A. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Khafizov, K. / Lafleur, J. / Love, J.D. / Stead, M. / Seidel, R. / Toro, R. / Almo, S.C.
History
DepositionSep 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Apr 3, 2024Group: 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,2218
Polymers55,7132
Non-polymers5086
Water1,20767
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)84,1459
Polymers83,5693
Non-polymers5766
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation11_566y,-z+1,-x+11
Buried area7120 Å2
ΔGint-129 kcal/mol
Surface area27810 Å2
MethodPISA
2
B: Enoyl-CoA hydratase/isomerase family protein
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)84,51815
Polymers83,5693
Non-polymers94912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation11_566y,-z+1,-x+11
Buried area7780 Å2
ΔGint-138 kcal/mol
Surface area24740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.883, 154.883, 154.883
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-301-

SO4

21A-301-

SO4

31A-302-

SO4

41A-302-

SO4

51B-301-

SO4

61B-302-

SO4

71B-302-

SO4

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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: 27856.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: echA3, MT0660, Rv0632c / Plasmid: CHS30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL / References: UniProt: P96907, enoyl-CoA hydratase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, Reservoir (Crystal Screen F11: 1.6 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane), Cryoprotection (30% ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, Reservoir (Crystal Screen F11: 1.6 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane), Cryoprotection (30% Ethylene glycol), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2012 / Details: MIRRORS
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.51→50 Å / Num. all: 21213 / Num. obs: 21213 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.9 % / Biso Wilson estimate: 62 Å2 / Rsym value: 0.1 / Net I/σ(I): 27.07
Reflection shellResolution: 2.51→2.55 Å / Redundancy: 21 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 1054 / Rsym value: 0.977 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0025refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data reduction
SCALEPACKdata scaling
SHELXCphasing
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD
Starting model: Built using Buccaneer

Resolution: 2.51→41.43 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 8.841 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.372 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 1090 5.1 %RANDOM
Rwork0.1823 ---
obs0.1856 21189 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.17 Å2 / Biso mean: 58.8883 Å2 / Biso min: 28.54 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.51→41.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3461 0 28 67 3556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193601
X-RAY DIFFRACTIONr_bond_other_d0.0010.023499
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.984886
X-RAY DIFFRACTIONr_angle_other_deg0.80338005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4765483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11423.464153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.82915530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7651528
X-RAY DIFFRACTIONr_chiral_restr0.080.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024166
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02828
LS refinement shellResolution: 2.513→2.578 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 89 -
Rwork0.24 1472 -
all-1561 -
obs--100 %

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