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- PDB-3pea: Crystal structure of enoyl-CoA hydratase from Bacillus anthracis ... -

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Basic information

Entry
Database: PDB / ID: 3pea
TitleCrystal structure of enoyl-CoA hydratase from Bacillus anthracis str. 'Ames Ancestor'
ComponentsEnoyl-CoA hydratase/isomerase family protein
KeywordsISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Fatty acid and phospholipid metabolism / enoyl-CoA / Bacillus anthracis
Function / homology
Function and homology information


enoyl-CoA hydratase / isomerase activity
Similarity search - Function
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 / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CITRATE ANION / Enoyl-CoA hydratase / Enoyl-CoA hydratase/isomerase family protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.817 Å
AuthorsFilippova, E.V. / Wawrzak, Z. / Kudritska, M. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of enoyl-CoA hydratase from Bacillus anthracis str. 'Ames Ancestor'
Authors: Filippova, E.V. / Wawrzak, Z. / Kudritska, M. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 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

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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
B: Enoyl-CoA hydratase/isomerase family protein
C: Enoyl-CoA hydratase/isomerase family protein
D: Enoyl-CoA hydratase/isomerase family protein
E: Enoyl-CoA hydratase/isomerase family protein
F: Enoyl-CoA hydratase/isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,87016
Polymers171,2196
Non-polymers1,65110
Water16,754930
1
A: Enoyl-CoA hydratase/isomerase family protein
B: Enoyl-CoA hydratase/isomerase family protein
C: Enoyl-CoA hydratase/isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4358
Polymers85,6103
Non-polymers8265
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9770 Å2
ΔGint-49 kcal/mol
Surface area28560 Å2
MethodPISA
2
D: Enoyl-CoA hydratase/isomerase family protein
E: Enoyl-CoA hydratase/isomerase family protein
F: Enoyl-CoA hydratase/isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4358
Polymers85,6103
Non-polymers8265
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9790 Å2
ΔGint-51 kcal/mol
Surface area28260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.954, 75.123, 89.490
Angle α, β, γ (deg.)89.04, 90.01, 75.47
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Enoyl-CoA hydratase/isomerase family protein


Mass: 28536.502 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS4420, BA_4761, GBAA4761, GBAA_4761 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q81L70, UniProt: A0A6L7GYV0*PLUS
#2: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 930 / 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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG3350, 0.2 M NH4 hydrogen Citrate, 2% PEG400, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.04006 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 23, 2010 / Details: MIRROR
RadiationMonochromator: Si(111) / Protocol: MOLECULAR REPLACEMENT / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04006 Å / Relative weight: 1
ReflectionResolution: 1.817→30 Å / Num. all: 151590 / Num. obs: 151590 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.9
Reflection shellResolution: 1.817→1.85 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.2 / Num. unique all: 7431 / % possible all: 95.7

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: the starting model was the structure solved by SAD in a different space group

Resolution: 1.817→29.016 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.135 / SU ML: 0.071 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19353 7600 5 %RANDOM
Rwork0.16211 ---
obs0.16369 143966 96.75 %-
all-143966 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.282 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å2-0.66 Å20.3 Å2
2---1.48 Å21.26 Å2
3----0.25 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.817→29.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11686 0 112 930 12728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02212071
X-RAY DIFFRACTIONr_bond_other_d0.0010.028166
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.96616279
X-RAY DIFFRACTIONr_angle_other_deg0.94319989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.58751551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11324.257498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.839152094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1841566
X-RAY DIFFRACTIONr_chiral_restr0.0920.21860
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213471
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022381
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_it0.8521.57681
X-RAY DIFFRACTIONr_mcbond_other0.2591.53186
X-RAY DIFFRACTIONr_mcangle_it1.567212288
X-RAY DIFFRACTIONr_scbond_it2.74434390
X-RAY DIFFRACTIONr_scangle_it4.5044.53991
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.817→1.864 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 538 -
Rwork0.24 9729 -
obs--88.31 %
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)
10.61230.123-0.20681.3343-0.21050.8054-0.05830.0939-0.0608-0.17320.0406-0.26530.02690.07890.01770.0357-0.00440.04680.0696-0.01910.067780.687473.938114.5508
20.56690.0104-0.3950.69820.30240.9803-0.0233-0.0754-0.11330.1264-0.0261-0.04820.1385-0.00510.04940.0635-0.0128-0.01320.0460.01480.030263.54859.994752.1702
30.96440.4597-0.65040.9536-0.23151.09990.1601-0.05820.13510.1399-0.04560.0058-0.24840.0003-0.11450.0807-0.00690.02580.0117-0.01390.035969.080393.511949.6267
40.50640.15320.12851.46450.22580.8065-0.07960.09150.0738-0.22260.04670.2821-0.0297-0.10440.03290.0609-0.0051-0.06740.08820.01290.077929.809670.036969.953
50.59430.01950.31740.7692-0.29640.8551-0.0106-0.06550.10720.0863-0.02370.0564-0.1128-0.00310.03430.0435-0.0110.00520.0494-0.02640.027346.753383.20896.7649
60.26230.31060.15820.60720.02380.63450.0917-0.0496-0.06870.084-0.02210.00730.20060.0026-0.06960.07380.0011-0.02580.05120.01130.065841.972650.731694.0989
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 257
2X-RAY DIFFRACTION2B1 - 257
3X-RAY DIFFRACTION3C0 - 257
4X-RAY DIFFRACTION4D1 - 257
5X-RAY DIFFRACTION5E1 - 257
6X-RAY DIFFRACTION6F1 - 267

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