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- PDB-4gjy: JMJD5 in complex with N-Oxalylglycine -

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Basic information

Entry
Database: PDB / ID: 4gjy
TitleJMJD5 in complex with N-Oxalylglycine
ComponentsJmjC domain-containing protein 5
KeywordsOXIDOREDUCTASE / JmjC / beta barrel / Fe(II) and 2-oxoglutarate binding
Function / homology
Function and homology information


[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / methylated histone binding / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization ...[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / methylated histone binding / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization / G2/M transition of mitotic cell cycle / p53 binding / chromosome / fibroblast proliferation / endopeptidase activity / in utero embryonic development / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of DNA-templated transcription / proteolysis / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Cupin-like domain 8 / Cupin-like domain / Cupin / 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
: / N-OXALYLGLYCINE / Bifunctional peptidase and arginyl-hydroxylase JMJD5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2492 Å
AuthorsDel Rizzo, P.A. / Trievel, R.C.
CitationJournal: Mol.Cell.Biol. / Year: 2012
Title: Crystal Structure and Functional Analysis of JMJD5 Indicate an Alternate Specificity and Function.
Authors: Del Rizzo, P.A. / Krishnan, S. / Trievel, R.C.
History
DepositionAug 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Nov 14, 2012Group: Structure summary
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: JmjC domain-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6093
Polymers27,4031
Non-polymers2062
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.818, 64.165, 76.865
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein JmjC domain-containing protein 5 / JmjC domain-containing protein 5 / Jumonji domain-containing protein 5


Mass: 27402.559 Da / Num. of mol.: 1 / Fragment: JmjC Domain (UNP Residues 183-416)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD5, KDM8 / Plasmid: pDR146 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(Rosetta2)
References: UniProt: Q8N371, [histone H3]-dimethyl-L-lysine36 demethylase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 4.5% PEG 3000, 0.1 M Bis-Tris pH 5.5, 0.05 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 3, 2010
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionRedundancy: 13.1 % / Av σ(I) over netI: 49.62 / Number: 892588 / Rmerge(I) obs: 0.073 / Χ2: 1.65 / D res high: 1.25 Å / D res low: 50 Å / Num. obs: 68062 / % possible obs: 98.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
2.865090.510.0493.77313.1
2.272.8699.710.0573.04613.8
1.982.2710010.0722.81114.2
1.81.9899.610.0872.12213.4
1.671.810010.1051.43114.7
1.571.6710010.1341.19314.6
1.51.5799.910.1711.00714.6
1.431.599.810.220.8514.4
1.381.4399.610.2720.78413.8
1.331.3899.410.320.76812.5
1.291.3399.410.3770.71210.3
1.251.2998.110.3990.6857.8
ReflectionResolution: 1.249→50 Å / Num. obs: 68062 / % possible obs: 98.8 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.073 / Χ2: 1.648 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.249-1.297.80.39955470.685198.1
1.29-1.3310.30.37756030.712199.4
1.33-1.3812.50.3256570.768199.4
1.38-1.4313.80.27256740.784199.6
1.43-1.514.40.2256480.85199.8
1.5-1.5714.60.17157071.007199.9
1.57-1.6714.60.13456851.1931100
1.67-1.814.70.10557231.4311100
1.8-1.9813.40.08757222.122199.6
1.98-2.2714.20.07257852.8111100
2.27-2.8613.80.05758153.046199.7
2.86-5013.10.04954963.773190.5

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.28 / FOM acentric: 0.29 / FOM centric: 0.23 / Reflection: 8389 / Reflection acentric: 7049 / Reflection centric: 1340
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-500.360.40.28411264147
4.5-7.10.370.390.31234947287
3.6-4.50.390.410.3965810155
3.1-3.60.340.360.2214901273217
2.7-3.10.240.250.1826592312347
2.5-2.70.160.160.1116301443187

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVE2.15phasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2492→30.43 Å / Occupancy max: 1 / Occupancy min: 0.16 / FOM work R set: 0.9373 / SU ML: 0.21 / σ(F): 0.13 / Phase error: 11.86 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1609 1971 2.94 %
Rwork0.1404 --
obs0.141 67095 97.3 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.432 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 48.91 Å2 / Biso mean: 14.2802 Å2 / Biso min: 4.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.4548 Å2-0 Å20 Å2
2---0.2821 Å2-0 Å2
3---0.7369 Å2
Refinement stepCycle: LAST / Resolution: 1.2492→30.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1853 0 11 344 2208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082037
X-RAY DIFFRACTIONf_angle_d1.252803
X-RAY DIFFRACTIONf_chiral_restr0.078296
X-RAY DIFFRACTIONf_plane_restr0.007367
X-RAY DIFFRACTIONf_dihedral_angle_d15.263772
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2492-1.28040.19641290.17964296442591
1.2804-1.31510.19241390.15114544468396
1.3151-1.35380.16381400.13034574471497
1.3538-1.39750.15111400.11744640478098
1.3975-1.44740.15271400.10554624476498
1.4474-1.50530.12571400.10144696483699
1.5053-1.57390.12971410.09614672481399
1.5739-1.65680.11691420.10014727486999
1.6568-1.76060.16061440.11174730487499
1.7606-1.89650.13811440.12444719486399
1.8965-2.08740.14441450.13324770491599
2.0874-2.38930.15651430.14094767491099
2.3893-3.00980.16041460.160848534999100
3.0098-30.43880.19631380.17174512465089

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