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- PDB-5nfo: Human JMJD7 in complex with Mn and 2OG in the P21212 form -

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Basic information

Entry
Database: PDB / ID: 5nfo
TitleHuman JMJD7 in complex with Mn and 2OG in the P21212 form
ComponentsJmjC domain-containing protein 7
KeywordsOXIDOREDUCTASE / NON-HEME / IRON / 2-OXOGLUTARATE / DIOXYGENASE / OXYGENASE / JMJC / JMJC DOMAIN / JmjC domain-containing protein 7 / JMJD7 / JMJC HYDROXYLASE / JMJC DEMETHYLASE / KDMS / POST-TRANSLATIONAL MODIFICATIONS / PTM / HYDROXYLATION / Lysyl hydroxylation / DIMERISATION / TRANSLATION FACTOR / DEVELOPMENTALLY REGULATED GTP BINDING PROTEINS / DRG1 / DRG2 / TRAFAC GTPase / HYPOXIA / NUCLEIC ACID-BINDING / METAL-BINDING / TRANSLATION / HELIX-LOOP-HELIX-BETA / DSBH / FACIAL TRIAD / DEVELOPMENT / CANCER / RIBOSOME BIOGENESIS
Function / homology
Function and homology information


peptidyl-lysine (3S)-dioxygenase / protein hydroxylation / peptidyl-lysine 3-dioxygenase activity / 2-oxoglutarate-dependent dioxygenase activity / Hydrolases; Acting on peptide bonds (peptidases) / aminopeptidase activity / monooxygenase activity / methylated histone binding / endopeptidase activity / proteolysis ...peptidyl-lysine (3S)-dioxygenase / protein hydroxylation / peptidyl-lysine 3-dioxygenase activity / 2-oxoglutarate-dependent dioxygenase activity / Hydrolases; Acting on peptide bonds (peptidases) / aminopeptidase activity / monooxygenase activity / methylated histone binding / endopeptidase activity / proteolysis / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Cupin-like domain 8 / Cupin-like domain / A domain family that is part of the cupin metalloenzyme superfamily. / Jelly Rolls / JmjC domain / JmjC domain profile. / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / NITRATE ION / Bifunctional peptidase and (3S)-lysyl hydroxylase JMJD7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.173 Å
AuthorsChowdhury, R. / Markolovic, S. / Schofield, C.J.
CitationJournal: To Be Published
Title: (3S)-Lysyl hydroxylation of TRAFAC GTPases is catalyzed by the human Jumonji-C oxygenase JMJD7.
Authors: Markolovic, S. / Zhuang, Q. / Wilkins, S.E. / Eaton, C. / Katz, M.J. / Smith, H.E. / Lesniak, R.K. / Hall, C. / Struwe, W.B. / Konietzny, R. / Davis, S. / Yang, M. / Ge, W. / Benesch, J.L. / ...Authors: Markolovic, S. / Zhuang, Q. / Wilkins, S.E. / Eaton, C. / Katz, M.J. / Smith, H.E. / Lesniak, R.K. / Hall, C. / Struwe, W.B. / Konietzny, R. / Davis, S. / Yang, M. / Ge, W. / Benesch, J.L. / Kessler, B.M. / Ratcliffe, P.J. / Cockman, M.E. / Fischer, R. / Wappner, P. / Chowdhury, R. / Coleman, M.L. / Schofield, C.J.
History
DepositionMar 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.2Jan 17, 2024Group: 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
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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: JmjC domain-containing protein 7
B: JmjC domain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,98714
Polymers75,9082
Non-polymers1,07912
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Homodimeric in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-52 kcal/mol
Surface area24840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.315, 61.020, 86.055
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein JmjC domain-containing protein 7 / Jumonji domain-containing protein 7


Mass: 37954.074 Da / Num. of mol.: 2 / Mutation: R260C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD7 / Plasmid: PET28A(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: P0C870

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Non-polymers , 5 types, 320 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 26 mg/mL His6-JMJD7-R260C, 2 mM MnCl2, 4 mM 2OG, 1.5 M Sodium Nitrate, 0.1 M Sodium Acetate pH 4.6 and additives (0.25% beta-NADP, 0.25% ATP, 0.25% N-Acetyl-D-galactosamine, 0.25% Gentamicin ...Details: 26 mg/mL His6-JMJD7-R260C, 2 mM MnCl2, 4 mM 2OG, 1.5 M Sodium Nitrate, 0.1 M Sodium Acetate pH 4.6 and additives (0.25% beta-NADP, 0.25% ATP, 0.25% N-Acetyl-D-galactosamine, 0.25% Gentamicin sulfate, 0.02 M HEPES-Na pH 6.8)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 19, 2016 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.17→49.776 Å / Num. obs: 38951 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 13.2857
Reflection shellResolution: 2.17→2.23 Å / Redundancy: 9.2 % / Rmerge(I) obs: 1.176 / Mean I/σ(I) obs: 1.75 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000706Edata reduction
HKL-2000706Edata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NFN

5nfn


Resolution: 2.173→49.776 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 1919 4.93 %
Rwork0.171 --
obs0.1728 38901 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.2 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 46 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2--11.57 Å20 Å2
3----10.7 Å2
Refinement stepCycle: LAST / Resolution: 2.173→49.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5025 0 66 308 5399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015309
X-RAY DIFFRACTIONf_angle_d1.217275
X-RAY DIFFRACTIONf_dihedral_angle_d13.9663150
X-RAY DIFFRACTIONf_chiral_restr0.048775
X-RAY DIFFRACTIONf_plane_restr0.005951
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1727-2.22710.31621420.26942589X-RAY DIFFRACTION100
2.2271-2.28730.28221400.24952596X-RAY DIFFRACTION100
2.2873-2.35460.24361410.24422604X-RAY DIFFRACTION100
2.3546-2.43060.24661340.22492578X-RAY DIFFRACTION100
2.4306-2.51740.26381560.22282603X-RAY DIFFRACTION100
2.5174-2.61820.27231130.2132639X-RAY DIFFRACTION100
2.6182-2.73740.22751540.19572590X-RAY DIFFRACTION100
2.7374-2.88170.22511000.17942658X-RAY DIFFRACTION100
2.8817-3.06220.17691370.17552647X-RAY DIFFRACTION100
3.0622-3.29860.21051350.15832620X-RAY DIFFRACTION100
3.2986-3.63050.17181570.14792642X-RAY DIFFRACTION100
3.6305-4.15560.17221410.13012669X-RAY DIFFRACTION100
4.1556-5.23470.15591300.12182711X-RAY DIFFRACTION100
5.2347-49.78930.23731390.18852836X-RAY DIFFRACTION100

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