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- PDB-4og1: Crystal Structure of a Putative Enoyl-CoA Hydratase from Novosphi... -

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Basic information

Entry
Database: PDB / ID: 4og1
TitleCrystal Structure of a Putative Enoyl-CoA Hydratase from Novosphingobium aromaticivorans DSM 12444
ComponentsEnoyl-CoA hydratase/isomerase
KeywordsLYASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / enoyl-CoA hydratase
Function / homology
Function and homology information


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, 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 ...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, 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Enoyl-CoA hydratase/isomerase
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsChapman, H.C. / Cooper, D.R. / Tkaczuk, K.L. / Cymborowski, M.T. / Stead, M. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Seidel, R. / Alkire, R. ...Chapman, H.C. / Cooper, D.R. / Tkaczuk, K.L. / Cymborowski, M.T. / Stead, M. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Seidel, R. / Alkire, R. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal Structure of a Putative Enoyl-CoA Hydratase from Novosphingobium aromaticivorans DSM 12444
Authors: Chapman, H.C. / Cooper, D.R. / Tkaczuk, K.L. / Cymborowski, M.T. / Stead, M. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Seidel, R. / Alkire, R. / Almo, S.C. / Minor, W.
History
DepositionJan 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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
Revision 1.2Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,1322
Polymers31,7621
Non-polymers3701
Water2,126118
1
A: Enoyl-CoA hydratase/isomerase
hetero molecules

A: Enoyl-CoA hydratase/isomerase
hetero molecules

A: Enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3976
Polymers95,2863
Non-polymers1,1113
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area13660 Å2
ΔGint-47 kcal/mol
Surface area27450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.587, 108.587, 108.587
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23

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Components

#1: Protein Enoyl-CoA hydratase/isomerase


Mass: 31762.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: Saro_0502 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q2GB23, enoyl-CoA hydratase
#2: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Polyethylene glycol


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.36 Å3/Da / Density % sol: 63.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Potassium Sulfate, 20% (w/v) PEG 3350, Equilibrated against reservoir of 1.5M NaCl , pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97936 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 11, 2013
RadiationMonochromator: Si (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 26899 / % possible obs: 99 %
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 9.1 % / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-3000data collection
SHELXSphasing
REFMAC5.8.0049refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.298 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19652 1341 5 %RANDOM
Rwork0.16664 ---
obs0.16813 25312 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.159 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 25 118 2091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192017
X-RAY DIFFRACTIONr_bond_other_d0.0010.021940
X-RAY DIFFRACTIONr_angle_refined_deg1.9821.9472718
X-RAY DIFFRACTIONr_angle_other_deg0.92834438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4615257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18422.90393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13515326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0471520
X-RAY DIFFRACTIONr_chiral_restr0.1180.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022300
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02474
X-RAY DIFFRACTIONr_mcbond_it2.1552.4411028
X-RAY DIFFRACTIONr_mcbond_other2.1562.441027
X-RAY DIFFRACTIONr_mcangle_it2.8253.6391282
X-RAY DIFFRACTIONr_mcangle_other2.8253.6411283
X-RAY DIFFRACTIONr_scbond_it3.6642.902985
X-RAY DIFFRACTIONr_scbond_other3.6152.902985
X-RAY DIFFRACTIONr_scangle_other5.1564.1681433
X-RAY DIFFRACTIONr_long_range_B_refined8.62520.9482293
X-RAY DIFFRACTIONr_long_range_B_other8.59320.512264
LS refinement shellResolution: 2.054→2.107 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 105 -
Rwork0.248 1855 -
obs--99.85 %
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)
13.0302-0.2619-0.66673.0959-0.59983.21080.11370.0390.5085-0.3489-0.01760.2405-0.7098-0.3093-0.0960.4830.23560.02440.13020.04710.26176.4945.67811.351
22.05-0.4725-0.37711.8921-0.25720.90290.04490.02520.3126-0.2503-0.0419-0.2368-0.3944-0.0812-0.0030.31690.09340.07080.06420.05010.147818.69634.98611.599
31.06920.09470.33411.9771-0.1772.01270.0254-0.27650.07760.2044-0.02530.1813-0.3538-0.3631-0.00010.18640.14210.06010.20730.01250.06726.84430.43126.989
414.64812.5701-1.382411.9006-3.88022.43350.0958-0.29230.35380.34120.08850.253-0.1514-0.2485-0.18430.23080.21250.09650.3781-0.02250.1487-6.13837.90934.355
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 72
2X-RAY DIFFRACTION2A84 - 175
3X-RAY DIFFRACTION3A176 - 260
4X-RAY DIFFRACTION4A261 - 268

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