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- PDB-3i47: CRYSTAL STRUCTURE OF putative enoyl CoA hydratase/isomerase (crot... -

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Basic information

Entry
Database: PDB / ID: 3i47
TitleCRYSTAL STRUCTURE OF putative enoyl CoA hydratase/isomerase (crotonase) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
ComponentsEnoyl CoA hydratase/isomerase (Crotonase)
KeywordsLYASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / crotonase / Isomerase / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


isoprenoid catabolic process / enoyl-CoA hydratase / enoyl-CoA hydratase activity / isomerase activity
Similarity search - Function
: / 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 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex ...: / 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 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Enoyl CoA hydratase/isomerase (Crotonase)
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.58 Å
AuthorsMalashkevich, V.N. / Toro, R. / Morano, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF putative enoyl CoA hydratase/isomerase (crotonase) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Authors: Malashkevich, V.N. / Toro, R. / Morano, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJul 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Oct 24, 2012Group: Structure summary
Revision 1.3Nov 1, 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 1.4Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.6Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl CoA hydratase/isomerase (Crotonase)


Theoretical massNumber of molelcules
Total (without water)29,5851
Polymers29,5851
Non-polymers00
Water6,287349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Enoyl CoA hydratase/isomerase (Crotonase)

A: Enoyl CoA hydratase/isomerase (Crotonase)

A: Enoyl CoA hydratase/isomerase (Crotonase)


Theoretical massNumber of molelcules
Total (without water)88,7543
Polymers88,7543
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area12500 Å2
ΔGint-98 kcal/mol
Surface area29970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.596, 124.596, 150.395
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-269-

HOH

21A-340-

HOH

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Components

#1: Protein Enoyl CoA hydratase/isomerase (Crotonase)


Mass: 29584.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / Gene: lpg1828 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q5ZUH0, enoyl-CoA hydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 3.8 Å3/Da / Density % sol: 67.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 35% Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 7.9 % / Av σ(I) over netI: 41.3 / Number: 911003 / Rmerge(I) obs: 0.086 / Χ2: 2.59 / D res high: 1.6 Å / D res low: 50 Å / Num. obs: 115033 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.345099.210.0474.5258.1
3.454.3410010.0576.0877.7
3.013.4510010.0776.4178
2.743.0110010.0875.3368
2.542.7410010.0893.8468
2.392.5410010.0943.3138
2.272.3910010.1012.9918
2.172.2710010.1082.7138
2.092.1710010.1252.3558
2.022.0910010.1442.0118
1.952.0210010.1681.7478
1.91.9510010.2061.4928
1.851.910010.2541.3268
1.81.8510010.3011.1827.9
1.761.810010.3741.1097.9
1.721.7610010.4461.0617.9
1.691.7210010.5391.0267.9
1.661.6910010.6171.0057.9
1.631.6610010.7070.9757.8
1.61.6399.910.7950.9467.2
ReflectionResolution: 1.58→50 Å / Num. obs: 115033 / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.086 / Χ2: 2.585 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.637.20.79557480.946199.9
1.63-1.667.80.70757360.9751100
1.66-1.697.90.61757471.0051100
1.69-1.727.90.53957451.0261100
1.72-1.767.90.44657881.0611100
1.76-1.87.90.37457081.1091100
1.8-1.857.90.30157451.1821100
1.85-1.980.25457821.3261100
1.9-1.9580.20657661.4921100
1.95-2.0280.16857081.7471100
2.02-2.0980.14458202.0111100
2.09-2.1780.12557302.3551100
2.17-2.2780.10857482.7131100
2.27-2.3980.10157522.9911100
2.39-2.5480.09457773.3131100
2.54-2.7480.08957463.8461100
2.74-3.0180.08757475.3361100
3.01-3.4580.07757476.4171100
3.45-4.347.70.05757656.0871100
4.34-508.10.04757284.525199.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.58→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.177 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.916 / SU B: 2.426 / SU ML: 0.035 / SU R Cruickshank DPI: 0.013 / SU Rfree: 0.013 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.013 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.179 2987 5.1 %RANDOM
Rwork0.168 ---
obs0.168 59026 95.9 %-
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: 69.23 Å2 / Biso mean: 20.601 Å2 / Biso min: 8.98 Å2
Baniso -1Baniso -2Baniso -3
1--3.45 Å20 Å20 Å2
2---3.45 Å20 Å2
3---6.91 Å2
Refinement stepCycle: LAST / Resolution: 1.58→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1993 0 0 349 2342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222062
X-RAY DIFFRACTIONr_angle_refined_deg1.091.9622795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1095268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.00224.94693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6915372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2861512
X-RAY DIFFRACTIONr_chiral_restr0.0760.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211542
X-RAY DIFFRACTIONr_mcbond_it0.8753.51303
X-RAY DIFFRACTIONr_mcangle_it2.53502094
X-RAY DIFFRACTIONr_scbond_it4.82150759
X-RAY DIFFRACTIONr_scangle_it1.2614.5696
LS refinement shellResolution: 1.578→1.619 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 93 -
Rwork0.322 1951 -
all-2044 -
obs--45.25 %
Refinement TLS params.Method: refined / Origin x: 44.55 Å / Origin y: 41.3933 Å / Origin z: 69.8381 Å
111213212223313233
T0.0063 Å20.0019 Å20.0017 Å2-0.0104 Å2-0.0041 Å2--0.0271 Å2
L0.2921 °2-0.1328 °2-0.0485 °2-0.8213 °2-0.0319 °2--0.0528 °2
S-0.0131 Å °-0.0329 Å °0.0121 Å °0.0037 Å °0.0255 Å °0.0979 Å °0.0138 Å °0.0011 Å °-0.0124 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 260
2X-RAY DIFFRACTION1A269 - 617

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