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- PDB-4jwv: Crystal Structure of putative short chain enoyl-CoA hydratase fro... -

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Basic information

Entry
Database: PDB / ID: 4jwv
TitleCrystal Structure of putative short chain enoyl-CoA hydratase from Novosphingobium aromaticivorans DSM 12444
ComponentsShort chain enoyl-CoA hydratase
KeywordsLYASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / PFAM PF00378
Function / homology
Function and homology information


enoyl-CoA hydratase / enoyl-CoA hydratase 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, 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
Short chain enoyl-CoA hydratase
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsCooper, D.R. / Mikolajczak, K. / Cymborowski, M. / Grabowski, M. / Ahmed, M. / Stead, M. / Hillerich, B. / Seidel, R. / Zimmerman, M. / Bonanno, J.B. ...Cooper, D.R. / Mikolajczak, K. / Cymborowski, M. / Grabowski, M. / Ahmed, M. / Stead, M. / Hillerich, B. / Seidel, R. / Zimmerman, M. / Bonanno, J.B. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal Structure of putative short chain enoyl-CoA hydratase from Novosphingobium aromaticivorans DSM 12444
Authors: Cooper, D.R. / Mikolajczak, K. / Cymborowski, M. / Grabowski, M. / Ahmed, M. / Stead, M. / Hillerich, B. / Seidel, R. / Zimmerman, M. / Bonanno, J.B. / Almo, S.C. / Minor, W.
History
DepositionMar 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 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 1.2Apr 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Short chain enoyl-CoA hydratase
B: Short chain enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)60,6372
Polymers60,6372
Non-polymers00
Water6,269348
1
A: Short chain enoyl-CoA hydratase
B: Short chain enoyl-CoA hydratase

A: Short chain enoyl-CoA hydratase
B: Short chain enoyl-CoA hydratase

A: Short chain enoyl-CoA hydratase
B: Short chain enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)181,9106
Polymers181,9106
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area23290 Å2
ΔGint-130 kcal/mol
Surface area53590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.311, 116.311, 116.311
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-311-

HOH

21A-412-

HOH

31B-334-

HOH

41B-357-

HOH

51B-439-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A3 - 256
2010B3 - 256
DetailsEach monomer in the ASU is 1/3 of a trimer that is 1/2 of a hexamer.

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Components

#1: Protein Short chain enoyl-CoA hydratase


Mass: 30318.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: Saro_1463 / Plasmid: pSGC-His_L-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q2G8B7, enoyl-CoA hydratase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: The drop was 200 nl 13.75 mg/ml protein mixed with 200 nl Qiagen Cryos Suite condition A4 (4.25 % isopropanol, 1.7 M Ammonium Sulfate, 15% glycerol). The crystallization reservoir contained ...Details: The drop was 200 nl 13.75 mg/ml protein mixed with 200 nl Qiagen Cryos Suite condition A4 (4.25 % isopropanol, 1.7 M Ammonium Sulfate, 15% glycerol). The crystallization reservoir contained only 1.5 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 9, 2013
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionRedundancy: 11.1 % / Av σ(I) over netI: 35.66 / Number: 458154 / Rmerge(I) obs: 0.098 / Χ2: 0.92 / D res high: 1.9 Å / D res low: 40 Å / Num. obs: 41251 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.154099.810.0320.54411.6
4.095.1510010.0651.35112.3
3.584.0910010.0711.42112.4
3.253.5810010.0650.98912.4
3.023.2510010.0730.89612.5
2.843.0210010.0950.91912.5
2.72.8410010.1210.90112.5
2.582.710010.1510.89412.5
2.482.5810010.1960.90112.5
2.392.4810010.2350.87912.5
2.322.3910010.2780.8912.5
2.252.3210010.3590.86712.5
2.192.2510010.4350.86112.5
2.142.1910010.5480.83912.4
2.092.1410010.6420.85812.3
2.052.0910010.7910.86810.1
2.012.0597.810.8810.8158.3
1.972.0197.410.7926.9
1.931.9797.610.7955.7
1.91.9397.710.8284.8
ReflectionResolution: 2.1→40 Å / Num. obs: 30946 / % possible obs: 100 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.116 / Χ2: 1.721 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.14120.77315250.5011100
2.14-2.1812.20.71315180.5091100
2.18-2.2212.40.63415170.5161100
2.22-2.2612.40.53815480.551100
2.26-2.3112.50.45815310.5731100
2.31-2.3712.50.38215210.6051100
2.37-2.4212.50.33615660.651100
2.42-2.4912.50.28815170.6961100
2.49-2.5612.50.2515120.7321100
2.56-2.6512.50.20715560.8271100
2.65-2.7412.60.17915410.9341100
2.74-2.8512.50.1515321.1121100
2.85-2.9812.50.13315511.381100
2.98-3.1412.50.10515571.6181100
3.14-3.3312.40.09615322.0931100
3.33-3.5912.30.08515412.7521100
3.59-3.95120.08215663.8031100
3.95-4.5211.60.07515644.3721100
4.52-5.711.70.07215944.7581100
5.7-4011.10.06716575.8871100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→38.8 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1731 / WRfactor Rwork: 0.1394 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.9125 / SU B: 6.302 / SU ML: 0.088 / SU R Cruickshank DPI: 0.1711 / SU Rfree: 0.1437 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1793 1552 5 %RANDOM
Rwork0.141 ---
obs0.1429 30862 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.25 Å2 / Biso mean: 35.1945 Å2 / Biso min: 20.27 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3767 0 0 348 4115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193844
X-RAY DIFFRACTIONr_bond_other_d0.0060.023742
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.975212
X-RAY DIFFRACTIONr_angle_other_deg1.10138559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1295504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83423.688160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73615584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.9631530
X-RAY DIFFRACTIONr_chiral_restr0.1140.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214421
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02853
Refine LS restraints NCS

Ens-ID: 1 / Number: 14449 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 96 -
Rwork0.156 2171 -
all-2267 -
obs--100 %
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)
10.5364-0.0625-0.10420.5284-0.08440.5158-0.01480.028-0.1441-0.0701-0.0029-0.05390.09030.04510.01780.07950.0210.02180.0476-0.01210.096334.9948.35921.153
20.45050.1891-0.0240.5919-0.090.4076-0.0070.0055-0.0596-0.02720.0095-0.1551-0.00140.0605-0.00250.01930.00890.00850.03920.00270.08957.24432.09538.748
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 257
2X-RAY DIFFRACTION2B4 - 257

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