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- PDB-4jyj: Crystal Structure of putative enoyl-CoA hydratase/isomerase from ... -

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Basic information

Entry
Database: PDB / ID: 4jyj
TitleCrystal Structure of putative enoyl-CoA hydratase/isomerase from Novosphingobium aromaticivorans DSM 12444
ComponentsEnoyl-CoA hydratase/isomerase
KeywordsISOMERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily / PFAM PF00378
Function / homology
Function and homology information


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
Unknown ligand / Enoyl-CoA hydratase/isomerase
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsCooper, D.R. / Porebski, P.J. / Domagalski, M.J. / Ahmed, M. / Stead, M. / Hillerich, B. / Seidel, R. / Zimmerman, M. / Bonanno, J.B. / Almo, S.C. ...Cooper, D.R. / Porebski, P.J. / Domagalski, M.J. / 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 enoyl-CoA hydratase/isomerase from Novosphingobium aromaticivorans DSM 12444
Authors: Cooper, D.R. / Porebski, P.J. / Domagalski, M.J. / Ahmed, M. / Stead, M. / Hillerich, B. / Seidel, R. / Zimmerman, M. / Bonanno, J.B. / Almo, S.C. / Minor, W. / New York Structural Genomics ...Authors: Cooper, D.R. / Porebski, P.J. / Domagalski, M.J. / 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)
History
DepositionMar 29, 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

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Assembly

Deposited unit
A: Enoyl-CoA hydratase/isomerase
B: Enoyl-CoA hydratase/isomerase


Theoretical massNumber of molelcules
Total (without water)66,0184
Polymers66,0182
Non-polymers02
Water3,207178
1
A: Enoyl-CoA hydratase/isomerase
B: Enoyl-CoA hydratase/isomerase

A: Enoyl-CoA hydratase/isomerase
B: Enoyl-CoA hydratase/isomerase

A: Enoyl-CoA hydratase/isomerase
B: Enoyl-CoA hydratase/isomerase


Theoretical massNumber of molelcules
Total (without water)198,05312
Polymers198,0536
Non-polymers06
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area29130 Å2
ΔGint-184 kcal/mol
Surface area47450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.697, 112.697, 112.697
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-449-

HOH

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

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A7 - 273
2010B7 - 273

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Components

#1: Protein Enoyl-CoA hydratase/isomerase


Mass: 33008.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: Saro_0518 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q2GB08
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsACCORDING TO THE AUTHORS THE UNKNOWN LIGANDS APPEAR TO BE A PHOSPHATE OR SULFATE, BUT NEITHER WAS ...ACCORDING TO THE AUTHORS THE UNKNOWN LIGANDS APPEAR TO BE A PHOSPHATE OR SULFATE, BUT NEITHER WAS PRESENT DURING PURIFICATION OR CRYSTALLIZATION

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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: 1.81 Å3/Da / Density % sol: 31.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: The drop was a mixture of 200 nl of 21.23 ml/ml protein with 200 nL of Hampton Research's Index HT condition G1 (25% PEG 3350, 200 mM NaCl, 100 mM Tris pH 8.5) equalibrated against a ...Details: The drop was a mixture of 200 nl of 21.23 ml/ml protein with 200 nL of Hampton Research's Index HT condition G1 (25% PEG 3350, 200 mM NaCl, 100 mM Tris pH 8.5) equalibrated against a reservoir of 2.5 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionRedundancy: 5.1 % / Number: 109153 / Rmerge(I) obs: 0.072 / Χ2: 0.91 / D res high: 2.3 Å / D res low: 40 Å / Num. obs: 21295 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.244098.810.0230.8965.3
4.956.2410010.0280.7665.9
4.334.9510010.031.0375.9
3.934.3310010.0320.8856
3.653.9310010.0410.9276
3.443.6510010.0510.8856
3.263.4410010.0740.8845.9
3.123.2610010.0960.8755.6
33.1210010.1110.885.4
2.9310010.1590.9115.2
2.812.910010.1860.9194.9
2.732.8110010.2330.9314.7
2.662.7399.910.2720.9484.6
2.592.6699.610.3110.9424.5
2.532.5999.510.3730.8954.4
2.482.5399.210.4230.9474.4
2.432.4899.510.4620.9154.4
2.382.4399.110.5850.9244.4
2.342.3898.810.6740.9614.4
2.32.3498.810.6410.9264.4
ReflectionResolution: 2.2→40 Å / Num. obs: 24422 / % possible obs: 99.4 % / Redundancy: 5 % / Rmerge(I) obs: 0.115
Reflection shellResolution: 2→2.24 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.72 / Num. unique all: 1177 / % possible all: 98.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→33.98 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.1804 / WRfactor Rwork: 0.1373 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8937 / SU B: 7.917 / SU ML: 0.103 / SU R Cruickshank DPI: 0.0596 / SU Rfree: 0.0418 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 1247 5.1 %RANDOM
Rwork0.1542 ---
obs0.1569 23109 99.44 %-
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: 99.01 Å2 / Biso mean: 39.3482 Å2 / Biso min: 21.83 Å2
Baniso -1Baniso -2Baniso -3
1--15.02 Å20.81 Å20.36 Å2
2--2.39 Å2-29.84 Å2
3---12.64 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4007 0 10 178 4195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194105
X-RAY DIFFRACTIONr_bond_other_d0.0050.023876
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.9555578
X-RAY DIFFRACTIONr_angle_other_deg1.15838878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27322.976168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.13115584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2941532
X-RAY DIFFRACTIONr_chiral_restr0.1040.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214730
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02954
Refine LS restraints NCS

Ens-ID: 1 / Number: 14664 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 77 -
Rwork0.199 1669 -
all-1746 -
obs--98.15 %
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)
10.07840.16970.05460.94740.29390.2089-0.04030.0814-0.0543-0.12180.0748-0.104-0.0185-0.0194-0.03450.101-0.02320.00260.1355-0.05070.060129.33822.75254.963
20.3120.03890.37860.14130.07040.4697-0.01460.02960.0105-0.09990.00050.0757-0.0280.01330.0140.0957-0.0039-0.03420.08910.01660.060218.3732.79559.517
31.38451.4651-0.14551.7096-0.03980.1751-0.0470.17430.0181-0.0150.1243-0.0053-0.0052-0.0264-0.07730.0618-0.00280.00570.09270.00150.052828.56727.31670.164
40.9837-0.7897-0.21660.7471-0.23721.66870.0480.0449-0.0116-0.1172-0.03840.03850.2311-0.0366-0.00970.0912-0.0477-0.05930.12840.00470.0872.99617.83658.582
50.18050.15320.14661.16460.0420.5019-0.01660.1364-0.0593-0.08360.0041-0.05850.04220.10890.01250.03210.00250.03680.1248-0.0230.084349.46314.85269.572
60.73590.4951-0.120.78060.16670.2435-0.0163-0.0584-0.10580.02310.0167-0.11080.04620.0952-0.00040.04160.043-0.01620.07210.00770.06849.54113.97585.016
71.26111.15140.14151.1822-0.0380.2719-0.0650.2124-0.0672-0.02470.1841-0.0127-0.01270.0175-0.1190.0676-0.01950.01820.065-0.01180.088637.46220.97777.85
80.49661.1984-1.02132.931-2.35714.79050.0196-0.0123-0.026-0.0490.1049-0.04850.30930.4918-0.12450.03940.03460.00250.26610.00280.132264.41429.06687.206
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 99
2X-RAY DIFFRACTION2A100 - 202
3X-RAY DIFFRACTION3A203 - 239
4X-RAY DIFFRACTION4A240 - 275
5X-RAY DIFFRACTION5B7 - 99
6X-RAY DIFFRACTION6B100 - 202
7X-RAY DIFFRACTION7B203 - 239
8X-RAY DIFFRACTION8B241 - 274

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