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- PDB-2opw: Crystal structure of human phytanoyl-CoA dioxygenase PHYHD1 (apo) -

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Basic information

Entry
Database: PDB / ID: 2opw
TitleCrystal structure of human phytanoyl-CoA dioxygenase PHYHD1 (apo)
ComponentsPHYHD1 protein
KeywordsOXIDOREDUCTASE / PHYHD1 / double-stranded beta helix / oxygenase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


phytanoyl-CoA dioxygenase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / 2-oxoglutarate-dependent dioxygenase activity / Oxidoreductases / dioxygenase activity / metal ion binding
Similarity search - Function
q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Phytanoyl-CoA dioxygenase domain-containing protein 1 / Phytanoyl-CoA dioxygenase domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhang, Z. / Butler, D. / McDonough, M.A. / Kavanagh, K.L. / Bray, J.E. / Ng, S.S. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. ...Zhang, Z. / Butler, D. / McDonough, M.A. / Kavanagh, K.L. / Bray, J.E. / Ng, S.S. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Sundstrom, M. / Schofield, C.J. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human phytanoyl-CoA dioxygenase PHYHD1 (apo)
Authors: Zhang, Z. / Butler, D. / McDonough, M.A. / Kavanagh, K.L. / Bray, J.E. / Ng, S.S. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Sundstrom, M. / Schofield, C.J. / Oppermann, U.
History
DepositionJan 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jun 27, 2018Group: Data collection / Derived calculations / Category: struct_conn
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS STATE THAT THE DISULFIDE BOND FORMED BETWEEN CRYSTALLOGRAPHICALLY RELATED MONOMERS VIA CYS3 IS PROBABLY NOT BIOLOGICALLY RELEVANT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHYHD1 protein


Theoretical massNumber of molelcules
Total (without water)32,4461
Polymers32,4461
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.970, 91.970, 81.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PHYHD1 protein / Phytanoyl-CoA dioxygenase domain containing 1


Mass: 32445.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Lung / Gene: PHYHD1 / Plasmid: pET / Production host: Escherichia coli (E. coli)
References: UniProt: Q7Z623, UniProt: Q5SRE7*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation ...References: UniProt: Q7Z623, UniProt: Q5SRE7*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.07 Å3/Da / Density % sol: 59.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 7% PEG3350, 200mM Calcium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9552 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 1, 2006
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9552 Å / Relative weight: 1
ReflectionResolution: 1.9→40.06 Å / Num. all: 31832 / Num. obs: 31832 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10
Reflection shellResolution: 1.9→2 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.24 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model built from sulfur SAD data

Resolution: 1.9→40.06 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 12.522 / SU ML: 0.161 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.143 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Extra density near SER 198 could not be identified and was left unmodelled
RfactorNum. reflection% reflectionSelection details
Rfree0.25793 1585 5 %RANDOM
Rwork0.2191 ---
all0.22108 29892 --
obs0.22108 29892 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.811 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20.47 Å20 Å2
2--0.95 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2214 0 0 111 2325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222285
X-RAY DIFFRACTIONr_bond_other_d0.0010.021546
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.9443105
X-RAY DIFFRACTIONr_angle_other_deg0.94133757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6375286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11223.333102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77215354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6891514
X-RAY DIFFRACTIONr_chiral_restr0.0870.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02485
X-RAY DIFFRACTIONr_nbd_refined0.2050.2441
X-RAY DIFFRACTIONr_nbd_other0.2010.21577
X-RAY DIFFRACTIONr_nbtor_refined0.1910.21100
X-RAY DIFFRACTIONr_nbtor_other0.0940.21218
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2110
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5730.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.26131542
X-RAY DIFFRACTIONr_mcbond_other0.923574
X-RAY DIFFRACTIONr_mcangle_it4.21452303
X-RAY DIFFRACTIONr_scbond_it6.7557931
X-RAY DIFFRACTIONr_scangle_it8.86611801
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 102 -
Rwork0.394 1975 -
obs--88.23 %
Refinement TLS params.Method: refined / Origin x: 29.1035 Å / Origin y: -30.7782 Å / Origin z: -4.3326 Å
111213212223313233
T-0.1116 Å2-0.1302 Å2-0.0253 Å2--0.0913 Å20.0249 Å2---0.1091 Å2
L1.8864 °20.3848 °2-0.6712 °2-2.2614 °2-0.2896 °2--2.7964 °2
S0.0866 Å °-0.0292 Å °0.0419 Å °-0.0222 Å °0.0428 Å °0.1878 Å °0.0587 Å °-0.2659 Å °-0.1294 Å °

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