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- PDB-4uir: Structure of oleate hydratase from Elizabethkingia meningoseptica -

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Basic information

Entry
Database: PDB / ID: 4uir
TitleStructure of oleate hydratase from Elizabethkingia meningoseptica
ComponentsOLEATE HYDRATASE
KeywordsLYASE
Function / homology
Function and homology information


oleate hydratase / oleate hydratase activity / response to fatty acid / FAD binding / fatty acid metabolic process / fatty acid binding / response to toxic substance
Similarity search - Function
D-Amino Acid Oxidase; Chain A, domain 2 - #80 / Oleate hydratase / MCRA family / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / Oleate hydratase
Similarity search - Component
Biological speciesELIZABETHKINGIA MENINGOSEPTICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsPavkov-Keller, T. / Hromic, A. / Engleder, M. / Emmerstorfer, A. / Steinkellner, G. / Schrempf, S. / Wriessnegger, T. / Leitner, E. / Strohmeier, G.A. / Kaluzna, I. ...Pavkov-Keller, T. / Hromic, A. / Engleder, M. / Emmerstorfer, A. / Steinkellner, G. / Schrempf, S. / Wriessnegger, T. / Leitner, E. / Strohmeier, G.A. / Kaluzna, I. / Mink, D. / Schuermann, M. / Wallner, S. / Macheroux, P. / Pichler, H. / Gruber, K.
CitationJournal: Chembiochem / Year: 2015
Title: Structure-Based Mechanism of Oleate Hydratase from Elizabethkingia Meningoseptica.
Authors: Engleder, M. / Pavkov-Keller, T. / Emmerstorfer, A. / Hromic, A. / Schrempf, S. / Steinkellner, G. / Wriessnegger, T. / Leitner, E. / Strohmeier, G.A. / Kaluzna, I. / Mink, D. / Schurmann, M. ...Authors: Engleder, M. / Pavkov-Keller, T. / Emmerstorfer, A. / Hromic, A. / Schrempf, S. / Steinkellner, G. / Wriessnegger, T. / Leitner, E. / Strohmeier, G.A. / Kaluzna, I. / Mink, D. / Schurmann, M. / Wallner, S. / Macheroux, P. / Gruber, K. / Pichler, H.
History
DepositionApr 2, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: OLEATE HYDRATASE
B: OLEATE HYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,3587
Polymers147,1492
Non-polymers1,2095
Water6,089338
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13360 Å2
ΔGint-78.7 kcal/mol
Surface area43590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.174, 143.930, 155.785
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein OLEATE HYDRATASE / FATTY ACID DOUBLE BOND HYDRATASE / FATTY ACID HYDRATASE / OHYA


Mass: 73574.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ELIZABETHKINGIA MENINGOSEPTICA (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: C7DLJ6, oleate hydratase

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Non-polymers , 5 types, 343 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSOME RESIDUES MISSING IN THE STRUCTURE (DISORDERED)

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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: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growDetails: 23.5MG/ML 10% W/V PEG 20,000; 20% V/V PEG MME 550, 0.03 M OF EACH HALIDE (0.3 M SODIUM FLUORIDE, 0.3 M SODIUM BROMIDE, 0.3 M SODIUM IODIDE) AND 0.1 M MOPS/HEPES-NA PH 7.5 (CONDITION B5, ...Details: 23.5MG/ML 10% W/V PEG 20,000; 20% V/V PEG MME 550, 0.03 M OF EACH HALIDE (0.3 M SODIUM FLUORIDE, 0.3 M SODIUM BROMIDE, 0.3 M SODIUM IODIDE) AND 0.1 M MOPS/HEPES-NA PH 7.5 (CONDITION B5, MORPHEUS SCREEN, MOLECULAR DIMENSIONS)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.75→48.8 Å / Num. obs: 49549 / % possible obs: 99.1 % / Observed criterion σ(I): 1.3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.24 / Net I/σ(I): 5.7
Reflection shellResolution: 2.75→2.92 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.3 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4IA5

4ia5


Resolution: 2.75→48.846 Å / SU ML: 0.36 / σ(F): 1.36 / Phase error: 24.16 / Stereochemistry target values: ML
Details: CHAIN A CONTAINS FAD AS COFACTOR AND IN CHAIN B IT IS PRESENT BUT NOT WITH HIGH OCCUPANCY AND IT COULD NOT BE FITTED IN THE ELECTRON DENSITY. AT THE C-TERMINUS OF CHAIN B THERE IS ALSO SOME ...Details: CHAIN A CONTAINS FAD AS COFACTOR AND IN CHAIN B IT IS PRESENT BUT NOT WITH HIGH OCCUPANCY AND IT COULD NOT BE FITTED IN THE ELECTRON DENSITY. AT THE C-TERMINUS OF CHAIN B THERE IS ALSO SOME ADDITIONAL DENSITY FOR UNIDENTIFIED LIGAND. IN CHAIN B THERE ARE SOME DISSORDERED REGIONS AA119-121, AA 624-626 AND AA642- -646. IN CHAIN A RESIDUES 619-623 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2495 2476 5 %
Rwork0.1948 --
obs0.1975 49519 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→48.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10227 0 79 338 10644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810540
X-RAY DIFFRACTIONf_angle_d0.96214265
X-RAY DIFFRACTIONf_dihedral_angle_d14.5573918
X-RAY DIFFRACTIONf_chiral_restr0.0411547
X-RAY DIFFRACTIONf_plane_restr0.0041831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.80290.34011330.27092524X-RAY DIFFRACTION97
2.8029-2.86010.34381340.27662560X-RAY DIFFRACTION99
2.8601-2.92230.3321370.28042590X-RAY DIFFRACTION99
2.9223-2.99030.36021370.26712595X-RAY DIFFRACTION99
2.9903-3.0650.34241350.25462567X-RAY DIFFRACTION99
3.065-3.14790.29861360.25472595X-RAY DIFFRACTION99
3.1479-3.24050.30271350.24252585X-RAY DIFFRACTION99
3.2405-3.34510.29961380.22852608X-RAY DIFFRACTION99
3.3451-3.46460.28151360.21022581X-RAY DIFFRACTION99
3.4646-3.60330.28181360.1982593X-RAY DIFFRACTION100
3.6033-3.76720.22841370.18482598X-RAY DIFFRACTION99
3.7672-3.96570.24811370.17082604X-RAY DIFFRACTION99
3.9657-4.21410.24061390.17492637X-RAY DIFFRACTION99
4.2141-4.53920.191370.14872605X-RAY DIFFRACTION99
4.5392-4.99560.17541390.14742644X-RAY DIFFRACTION99
4.9956-5.71750.20161410.15962672X-RAY DIFFRACTION100
5.7175-7.19980.21011410.17692689X-RAY DIFFRACTION99
7.1998-48.85410.20491480.16912796X-RAY DIFFRACTION99

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