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- PDB-4nhx: Crystal structure of human OGFOD1, 2-oxoglutarate and iron-depend... -

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Basic information

Entry
Database: PDB / ID: 4nhx
TitleCrystal structure of human OGFOD1, 2-oxoglutarate and iron-dependent oxygenase domain containing 1, in complex with N-oxalylglycine (NOG)
Components2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1
KeywordsOxidoreductase/Oxidoreductase inhibitor / jelly-roll fold / translation / ribosome / double-stranded beta helix / oxygen sensing / Oxidoreductase-Oxidoreductase inhibitor complex
Function / homology
Function and homology information


peptidyl-proline hydroxylation / peptidyl-proline 3-dioxygenase activity / protein hydroxylation / peptidyl-proline 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 / regulation of translational termination / L-ascorbic acid binding / Protein hydroxylation / stress granule assembly / cytoplasmic stress granule ...peptidyl-proline hydroxylation / peptidyl-proline 3-dioxygenase activity / protein hydroxylation / peptidyl-proline 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 / regulation of translational termination / L-ascorbic acid binding / Protein hydroxylation / stress granule assembly / cytoplasmic stress granule / cell population proliferation / iron ion binding / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain / Prolyl 3,4-dihydroxylase TPA1/OFD1, N-terminal domain / Oxoglutarate and iron-dependent oxygenase degradation C-term / 2OG-Fe(II) oxygenase superfamily / : / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. ...Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain / Prolyl 3,4-dihydroxylase TPA1/OFD1, N-terminal domain / Oxoglutarate and iron-dependent oxygenase degradation C-term / 2OG-Fe(II) oxygenase superfamily / : / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / N-OXALYLGLYCINE / Prolyl 3-hydroxylase OGFOD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.105 Å
AuthorsHorita, S. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Structure / Year: 2015
Title: Structure of the Ribosomal Oxygenase OGFOD1 Provides Insights into the Regio- and Stereoselectivity of Prolyl Hydroxylases.
Authors: Horita, S. / Scotti, J.S. / Thinnes, C. / Mottaghi-Taromsari, Y.S. / Thalhammer, A. / Ge, W. / Aik, W. / Loenarz, C. / Schofield, C.J. / McDonough, M.A.
History
DepositionNov 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.5Sep 20, 2023Group: 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 / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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 / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8175
Polymers65,4991
Non-polymers3174
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.401, 64.401, 232.041
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1 / Termination and polyadenylation 1 homolog


Mass: 65499.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGFOD1, KIAA1612, TPA1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli)
References: UniProt: Q8N543, 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

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Non-polymers , 5 types, 179 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.7 mM MnCl2, 1.0 mM OGA, 25% (w/v) PEG 1500, 100 mM MIB buffer and 100 mM glycine, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.8344 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2013
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8344 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 33393 / Num. obs: 33097 / % possible obs: 99.1 % / Redundancy: 16.2 % / Rmerge(I) obs: 0.153 / Net I/σ(I): 6.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.186.10.6482.5191.7
2.18-2.2610.10.5833199.2
2.26-2.3714.30.5094.51100
2.37-2.49180.42361100
2.49-2.6518.20.3448.51100
2.65-2.85190.267141100
2.85-3.1418.90.20214.81100
3.14-3.5919.20.16917.31100
3.59-4.52190.14518.51100
4.52-5017.90.1219.81100

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
HKL-3000data scaling
PHASERphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3KT7

3kt7


Resolution: 2.105→45.239 Å / Occupancy max: 1 / Occupancy min: 0.32 / SU ML: 0.23 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2154 2004 6.07 %Random
Rwork0.1887 ---
obs0.1904 33004 98.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.7004 Å2
Refinement stepCycle: LAST / Resolution: 2.105→45.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3734 0 18 175 3927
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d1
X-RAY DIFFRACTIONf_dihedral_angle_d
X-RAY DIFFRACTIONf_chiral_restr
X-RAY DIFFRACTIONf_plane_restr
LS refinement shellResolution: 2.1053→2.158 Å
RfactorNum. reflection% reflection
Rfree0.3383 119 -
Rwork0.2965 --
obs--85 %
Refinement TLS params.Method: refined / Origin x: -8.1162 Å / Origin y: 9.1731 Å / Origin z: 57.5758 Å
111213212223313233
T0.3728 Å20.05 Å2-0.0177 Å2-0.2654 Å2-0.0074 Å2--0.1957 Å2
L3.7739 °22.8039 °2-1.4561 °2-2.938 °2-1.2218 °2--1.0293 °2
S-0.0329 Å °-0.1718 Å °-0.0735 Å °-0.2621 Å °-0.1179 Å °-0.0032 Å °0.1248 Å °0.1517 Å °0.1652 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA24 - 542
2X-RAY DIFFRACTION1allA601 - 975

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