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- PDB-3opt: Crystal structure of the Rph1 catalytic core with a-ketoglutarate -

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Basic information

Entry
Database: PDB / ID: 3opt
TitleCrystal structure of the Rph1 catalytic core with a-ketoglutarate
ComponentsDNA damage-responsive transcriptional repressor RPH1
KeywordsOXIDOREDUCTASE / Rph1 / histone demethylase / catalytic core
Function / homology
Function and homology information


histone H3K36 demethylase activity / histone H3K9 demethylase activity / negative regulation of autophagy / positive regulation of transcription elongation by RNA polymerase II / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of gene expression / sequence-specific DNA binding / chromatin remodeling / chromatin / negative regulation of transcription by RNA polymerase II ...histone H3K36 demethylase activity / histone H3K9 demethylase activity / negative regulation of autophagy / positive regulation of transcription elongation by RNA polymerase II / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of gene expression / sequence-specific DNA binding / chromatin remodeling / chromatin / negative regulation of transcription by RNA polymerase II / nucleus / metal ion binding
Similarity search - Function
JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Zinc finger, C2H2 type / Cupin / JmjC domain, hydroxylase / zinc finger / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain ...JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Zinc finger, C2H2 type / Cupin / JmjC domain, hydroxylase / zinc finger / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / NICKEL (II) ION / DNA damage-responsive transcriptional repressor RPH1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsChang, Y. / Wu, J. / Tong, X. / Zhou, J. / Ding, J.
CitationJournal: Biochem.J. / Year: 2011
Title: Crystal structure of the catalytic core of Saccharomyces cerevesiae histone demethylase Rph1: insights into the substrate specificity and catalytic mechanism
Authors: Chang, Y. / Wu, J. / Tong, X.J. / Zhou, J.Q. / Ding, J.
History
DepositionSep 2, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references / Refinement description
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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: DNA damage-responsive transcriptional repressor RPH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8183
Polymers43,6141
Non-polymers2052
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.415, 109.415, 145.958
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein DNA damage-responsive transcriptional repressor RPH1


Mass: 43613.613 Da / Num. of mol.: 1 / Fragment: catalytic core domain, UNP residues 1-373
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPH1, YER169W / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P39956, [histone H3]-dimethyl-L-lysine36 demethylase
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 5.7828 Å3/Da / Density % sol: 78.7299 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M ammonium sulfate, 0.1M HEPES, 7% PFG 4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 21926 / % possible obs: 77.1 % / Redundancy: 7.5 % / Biso Wilson estimate: 31.78 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 21.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.34 / % possible all: 39.6

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
DiffractionAnisotropy Serverdata scaling
PHASESphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→39.74 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7919 / SU ML: 0.34 / σ(F): 1.33 / Phase error: 27.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2356 1092 4.98 %
Rwork0.1983 --
obs0.2003 21926 44.14 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.787 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso max: 137.24 Å2 / Biso mean: 41.6666 Å2 / Biso min: 6.29 Å2
Baniso -1Baniso -2Baniso -3
1--1.946 Å2-0 Å20 Å2
2---1.946 Å2-0 Å2
3---2.3415 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2464 0 11 226 2701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032551
X-RAY DIFFRACTIONf_angle_d0.6313459
X-RAY DIFFRACTIONf_chiral_restr0.045345
X-RAY DIFFRACTIONf_plane_restr0.003448
X-RAY DIFFRACTIONf_dihedral_angle_d16.364931
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2073-2.30770.381540.336289932
2.3077-2.42940.56190.30623874067
2.4294-2.58150.4131380.307273777513
2.5815-2.78080.2563630.31011282134522
2.7808-3.06050.34621050.26242108221336
3.0605-3.50310.29872250.23394449467475
3.5031-4.41230.20423340.180358566190100
4.4123-36.36050.20513040.17015926623099
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)
10.23040.12950.09060.52640.13680.5474-0.19-0.09270.1039-0.2016-0.2341-0.0026-0.04790.069-0.07820.1174-0.1779-0.1256-0.0014-0.2006-0.5232-47.807437.20480.6331
20.03740.0035-0.01520.0324-0.00070.01010.0196-0.03740.0566-0.0942-0.0177-0.02650.05750.0407-0.0157-0.2243-0.1821-0.0532-0.1052-0.00510.2816-47.503335.94880.3284
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 6:341)A6 - 341
2X-RAY DIFFRACTION2(chain A and resid 374:601)A374 - 601

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