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- PDB-4mou: Crystal Structure of an Enoyl-CoA Hydratase/Isomerase Family Memb... -

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Basic information

Entry
Database: PDB / ID: 4mou
TitleCrystal Structure of an Enoyl-CoA Hydratase/Isomerase Family Member, NYSGRC target 028282
ComponentsEnoyl-CoA hydratase/isomerase family protein
KeywordsISOMERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / Cronotase fold / enoyl-CoA hydratase/isomerase
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
CACODYLATE ION / Enoyl-CoA hydratase/isomerase family protein
Similarity search - Component
Biological speciesArthrobacter aurescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsChapman, H.C. / Cooper, D.R. / Geffken, K.T. / Cymborowski, M.T. / Osinski, T. / Stead, M. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Seidel, R. ...Chapman, H.C. / Cooper, D.R. / Geffken, K.T. / Cymborowski, M.T. / Osinski, T. / Stead, M. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Seidel, R. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal Structure of an Enoyl-CoA Hydratase/Isomerase Family Member, NYSGRC target 028282
Authors: Chapman, H.C. / Cooper, D.R. / Geffken, K.T. / Cymborowski, M.T. / Osinski, T. / Stead, M. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Seidel, R. / Almo, S.C. / Minor, W. / New York ...Authors: Chapman, H.C. / Cooper, D.R. / Geffken, K.T. / Cymborowski, M.T. / Osinski, T. / Stead, M. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Seidel, R. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
History
DepositionSep 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9276
Polymers95,5163
Non-polymers4113
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10480 Å2
ΔGint-77 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.455, 160.455, 178.691
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-549-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A9 - 273
2010B9 - 273
1020A13 - 272
2020C13 - 272
1030B13 - 272
2030C13 - 272

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 31838.695 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter aurescens (bacteria) / Strain: TC1 / Gene: AAur_3475 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: A1RAA6
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 3.01 Å3/Da / Density % sol: 59.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Calcium Acetate, 0.1M Cacodylate pH 6.5, 40% PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 19, 2013 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionRedundancy: 8.1 % / Number: 434352 / Rmerge(I) obs: 0.131 / Χ2: 0.88 / D res high: 2.25 Å / D res low: 40 Å / Num. obs: 53562 / % possible obs: 97.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.14098.410.0340.4329.3
4.846.199.310.0580.9029.8
4.234.8499.310.0771.3529.8
3.854.2399.710.091.3959.9
3.573.8599.710.0981.13610
3.363.5799.910.110.8989.9
3.193.3699.910.130.8339.7
3.053.1999.810.1660.7949.5
2.943.0599.610.2110.7889.2
2.832.9499.410.2630.7869
2.752.8399.310.3040.7898.7
2.672.7598.710.3390.7848.6
2.62.6798.510.3830.7858.3
2.532.697.910.4480.768
2.482.5397.610.4550.7577.1
2.422.4896.810.4250.7966.1
2.382.4293.110.4130.8215.1
2.332.3890.710.4130.8064.5
2.292.3388.210.4040.9053.9
2.252.2985.510.3930.7533.5
ReflectionResolution: 2.2→40 Å / Num. obs: 56774 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 1.95 / Num. unique all: 2437 / % possible all: 84.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→39.06 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.11 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 2728 5.1 %RANDOM
Rwork0.171 ---
obs0.173 51216 97.49 %-
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 max: 109.86 Å2 / Biso mean: 25.6398 Å2 / Biso min: 9.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2--0.53 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.25→39.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5735 0 15 565 6315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195858
X-RAY DIFFRACTIONr_bond_other_d0.0080.025687
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.9877964
X-RAY DIFFRACTIONr_angle_other_deg1.239313056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4595778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.28723.5220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51315868
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2131547
X-RAY DIFFRACTIONr_chiral_restr0.1040.2929
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216658
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021237
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A150810.06
12B150810.06
21A146060.07
22C146060.07
31B146880.07
32C146880.07
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 172 -
Rwork0.216 3294 -
all-3466 -
obs--86.13 %
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)
10.80820.2484-0.37761.2243-0.33312.9511-0.0181-0.0475-0.06230.2133-0.04670.09280.0379-0.07430.06490.09840.00950.06930.0437-0.00330.062621.06712.46839.069
20.1612-0.22060.05260.4521-0.25770.78050.0132-0.0315-0.01870.01410.01310.0620.04280.0272-0.02630.07390.02340.05150.05540.00850.050533.3473.35934.286
30.55920.38620.41960.84120.79433.14810.0304-0.0031-0.01470.062-0.0930.081-0.0122-0.1870.06270.03420.00490.02730.0520.01650.068330.39916.75316.183
43.08694.7025-1.62227.8392-1.83945.7130.18010.23520.28140.20610.1590.1736-0.7259-0.2385-0.33910.16220.04950.0320.10260.08080.137531.33430.57112.462
51.8936-0.927-0.15084.3034-0.16181.0527-0.03540.02760.1191-0.01620.00410.028-0.0413-0.00180.03120.04170.01340.02350.08110.05060.051854.99219.638-2.789
60.5941-0.1552-0.22540.9654-0.01840.1224-0.01610.0096-0.00780.0059-0.01790.04160.010.0230.03390.06860.00220.0320.07910.03650.052546.39215.2199.957
71.66631.19480.53562.65870.65480.9785-0.02810.0274-0.1273-0.0516-0.0267-0.1010.09750.02420.05480.06010.02850.0490.06640.03140.049557.732-2.2175.966
86.6093-1.8871.5656.1668-3.68744.72990.0574-0.0657-0.35-0.238-0.1224-0.34910.19820.26240.06510.12480.04380.12280.07460.01090.184569.392-10.4093.37
94.0046-0.3684-1.55881.64170.70252.6409-0.031-0.2003-0.37180.05150.0164-0.14360.24680.25290.01470.14220.09660.05480.07920.06540.120856.847-24.00329.177
100.8871-0.1603-0.42560.6580.19320.4862-0.05320.0171-0.09710.02260.0098-0.08150.08350.07140.04340.09720.04050.04590.04420.02340.054856.315-12.19518.64
112.49460.6521-0.44560.84330.06670.6310.0229-0.1005-0.04510.05130.01380.07510.07470.0214-0.03660.09630.03930.03550.04630.02210.040242.682-10.64632.79
123.9929-1.7573-1.41842.04-0.57235.4162-0.3189-0.2872-0.26470.30560.14320.5303-0.07340.24690.17570.10540.01030.07060.1460.06970.217333.039-14.94546.635
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 58
2X-RAY DIFFRACTION2A59 - 198
3X-RAY DIFFRACTION3A199 - 249
4X-RAY DIFFRACTION4A250 - 272
5X-RAY DIFFRACTION5B8 - 58
6X-RAY DIFFRACTION6B59 - 195
7X-RAY DIFFRACTION7B196 - 247
8X-RAY DIFFRACTION8B248 - 272
9X-RAY DIFFRACTION9C12 - 64
10X-RAY DIFFRACTION10C65 - 181
11X-RAY DIFFRACTION11C182 - 247
12X-RAY DIFFRACTION12C248 - 272

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