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- PDB-5odo: Crystal Structure of the Oleate hydratase of Rhodococcus erythropolis -

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Basic information

Entry
Database: PDB / ID: 5odo
TitleCrystal Structure of the Oleate hydratase of Rhodococcus erythropolis
ComponentsIsomerase
KeywordsLYASE / Hydratase / Rossmann fold / FAD binding / fatty acid / immune system
Function / homologyoleate hydratase activity / Oleate hydratase / MCRA family / isomerase activity / FAD binding / fatty acid metabolic process / FAD/NAD(P)-binding domain superfamily / FORMIC ACID / Isomerase
Function and homology information
Biological speciesRhodococcus erythropolis DN1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsDriller, R. / Lorenzen, J. / Waldow, A. / Qoura, F. / Brueck, T. / Loll, B.
CitationJournal: Chemcatchem / Year: 2017
Title: Rhodococcus erythropolis Oleate Hydratase: a New Member in the Oleate Hydratase Family Tree - Biochemical and Structural Studies.
Authors: Lorenzen, J. / Driller, R. / Waldow, A. / Quora, F. / Loll, B. / Brueck, T.
History
DepositionJul 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isomerase
B: Isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,93920
Polymers132,0622
Non-polymers87718
Water7,728429
1
A: Isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,56211
Polymers66,0311
Non-polymers53110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3789
Polymers66,0311
Non-polymers3468
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)261.747, 261.747, 127.304
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Isomerase


Mass: 66031.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis DN1 (bacteria)
Gene: N601_10635 / Production host: Escherichia coli (E. coli) / References: UniProt: T5I9M6*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 4.77 Å3/Da / Density % sol: 74.19 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 100 mM Bis-Tris/HCl 300 mM Magnesium formate 5% (v/v) glycerol
PH range: 5.5 - 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98141 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2016
RadiationMonochromator: SI111-DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98141 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 75230 / % possible obs: 99.8 % / Redundancy: 22.2 % / Net I/σ(I): 13.66

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ia5

4ia5


Resolution: 2.64→49.466 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.96
RfactorNum. reflection% reflection
Rfree0.2202 2097 2.79 %
Rwork0.1891 --
obs0.19 75185 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.64→49.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8534 0 54 429 9017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118867
X-RAY DIFFRACTIONf_angle_d0.84212003
X-RAY DIFFRACTIONf_dihedral_angle_d12.0335267
X-RAY DIFFRACTIONf_chiral_restr0.0581284
X-RAY DIFFRACTIONf_plane_restr0.0051564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6401-2.70150.35021350.31944748X-RAY DIFFRACTION99
2.7015-2.7690.35341380.29164805X-RAY DIFFRACTION100
2.769-2.84390.34161380.27954811X-RAY DIFFRACTION100
2.8439-2.92760.29951380.27284797X-RAY DIFFRACTION100
2.9276-3.02210.30231390.2544828X-RAY DIFFRACTION100
3.0221-3.13010.26361380.25274815X-RAY DIFFRACTION100
3.1301-3.25540.31081390.23134828X-RAY DIFFRACTION100
3.2554-3.40350.26771390.22174839X-RAY DIFFRACTION100
3.4035-3.58290.22141390.1984861X-RAY DIFFRACTION100
3.5829-3.80730.19771400.17584853X-RAY DIFFRACTION100
3.8073-4.10110.20731400.15884899X-RAY DIFFRACTION100
4.1011-4.51360.16891410.13544888X-RAY DIFFRACTION100
4.5136-5.16610.17821410.13424928X-RAY DIFFRACTION100
5.1661-6.50640.17791430.15984988X-RAY DIFFRACTION100
6.5064-49.47420.14851490.15815200X-RAY DIFFRACTION99

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