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- PDB-4igo: Histone H3 Lysine 4 Demethylating rice Rice JMJ703 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4igo
TitleHistone H3 Lysine 4 Demethylating rice Rice JMJ703 in complex with alpha-KG
ComponentsOs05g0196500 protein
KeywordsSTRUCTURAL PROTEIN / JumonjiC / Histone demethylase
Function / homology
Function and homology information


positive regulation of growth rate / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / histone H3K4 demethylase activity / negative regulation of gene expression, epigenetic / ferrous iron binding / regulation of gene expression / chromatin remodeling / chromatin / nucleus
Similarity search - Function
FY-rich, N-terminal / F/Y-rich N-terminus / FYR domain FYRN motif profile. / "FY-rich" domain, N-terminal region / FY-rich, C-terminal / F/Y rich C-terminus / FYR domain FYRC motif profile. / "FY-rich" domain, C-terminal region / Zinc finger, C5HC2-type / C5HC2 zinc finger ...FY-rich, N-terminal / F/Y-rich N-terminus / FYR domain FYRN motif profile. / "FY-rich" domain, N-terminal region / FY-rich, C-terminal / F/Y rich C-terminus / FYR domain FYRC motif profile. / "FY-rich" domain, C-terminal region / Zinc finger, C5HC2-type / C5HC2 zinc finger / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / Lysine-specific demethylase JMJ703
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChen, Q.F. / Chen, X.S. / Wang, Q. / Zhang, F.B. / Lou, Z.Y. / Zhang, Q.F. / Zhou, D.X.
CitationJournal: PLoS Genet. / Year: 2013
Title: Structural basis of a histone H3 lysine 4 demethylase required for stem elongation in rice.
Authors: Chen, Q. / Chen, X. / Wang, Q. / Zhang, F. / Lou, Z. / Zhang, Q. / Zhou, D.X.
History
DepositionDec 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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

Downloads & links

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Assembly

Deposited unit
A: Os05g0196500 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1703
Polymers40,9681
Non-polymers2022
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.518, 90.518, 76.048
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Os05g0196500 protein / Putative uncharacterized protein P0617H07.8 / Histone H3


Mass: 40968.012 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 139-498
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: P0617H07.8, Os05g0196500 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53WJ1
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: potassium phosphate monobasic, 25% (w/v) polyethylene glycol 8000 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBSRF 1W2B11
SYNCHROTRONSSRF BL17U21
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDJan 3, 2012
ADSC QUANTUM 3152CCDJan 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 16249 / Num. obs: 15149 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OQ6

2oq6


Resolution: 2.4→38.892 Å / SU ML: 0.68 / σ(F): 1.35 / Phase error: 26.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 684 4.91 %random
Rwork0.1934 ---
all0.1966 15149 --
obs0.1952 13938 99.92 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.279 Å2 / ksol: 0.288 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.4705 Å20 Å2-0 Å2
2--5.4705 Å20 Å2
3----10.9409 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 11 89 2308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092286
X-RAY DIFFRACTIONf_angle_d1.2683106
X-RAY DIFFRACTIONf_dihedral_angle_d16.843827
X-RAY DIFFRACTIONf_chiral_restr0.092315
X-RAY DIFFRACTIONf_plane_restr0.006403
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4003-2.58560.33241190.25192654
2.5856-2.84570.2951350.22822631
2.8457-3.25730.30031320.20942648
3.2573-4.10310.23211490.182647
4.1031-38.89750.18381490.17912674

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