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- PDB-2xdv: Crystal Structure of the Catalytic Domain of FLJ14393 -

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Entry
Database: PDB / ID: 2xdv
TitleCrystal Structure of the Catalytic Domain of FLJ14393
ComponentsMYC-INDUCED NUCLEAR ANTIGEN
KeywordsNUCLEAR PROTEIN / RIBOSOME BIOGENESIS
Function / homology
Function and homology information


protein-L-histidine (3S)-3-hydroxylase / peptidyl-histidine dioxygenase activity / histone H3K36 demethylase activity / histone H3K4 demethylase activity / Protein hydroxylation / histone demethylase activity / HDMs demethylate histones / transcription corepressor activity / ribosome biogenesis / transcription regulator complex ...protein-L-histidine (3S)-3-hydroxylase / peptidyl-histidine dioxygenase activity / histone H3K36 demethylase activity / histone H3K4 demethylase activity / Protein hydroxylation / histone demethylase activity / HDMs demethylate histones / transcription corepressor activity / ribosome biogenesis / transcription regulator complex / nucleolus / nucleoplasm / identical protein binding / metal ion binding / cytosol
Similarity search - Function
ROXA-like, winged helix / ROXA-like winged helix / JmjC domain-containing ribosomal oxygenase (ROX), dimer domain / Outer Surface Protein A; domain 3 - #40 / JmjC domain-containing / JmjC domain / Outer Surface Protein A; domain 3 / Cupin / JmjC domain / JmjC domain profile. ...ROXA-like, winged helix / ROXA-like winged helix / JmjC domain-containing ribosomal oxygenase (ROX), dimer domain / Outer Surface Protein A; domain 3 - #40 / JmjC domain-containing / JmjC domain / Outer Surface Protein A; domain 3 / Cupin / JmjC domain / JmjC domain profile. / Arc Repressor Mutant, subunit A / Jelly Rolls / Alpha-Beta Complex / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / : / NICKEL (II) ION / N-OXALYLGLYCINE / Ribosomal oxygenase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.57 Å
AuthorsKrojer, T. / Muniz, J.R.C. / Ng, S.S. / Pilka, E. / Guo, K. / Pike, A.C.W. / Filippakopoulos, P. / Knapp, S. / Kavanagh, K.L. / Gileadi, O. ...Krojer, T. / Muniz, J.R.C. / Ng, S.S. / Pilka, E. / Guo, K. / Pike, A.C.W. / Filippakopoulos, P. / Knapp, S. / Kavanagh, K.L. / Gileadi, O. / Bunkoczi, G. / Yue, W.W. / Niesen, F. / Sobott, F. / Fedorov, O. / Savitsky, P. / Kochan, G. / Daniel, M. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Oppermann, U.
CitationJournal: Nature / Year: 2014
Title: Ribosomal oxygenases are structurally conserved from prokaryotes to humans.
Authors: Chowdhury, R. / Sekirnik, R. / Brissett, N.C. / Krojer, T. / Ho, C.H. / Ng, S.S. / Clifton, I.J. / Ge, W. / Kershaw, N.J. / Fox, G.C. / Muniz, J.R.C. / Vollmar, M. / Phillips, C. / Pilka, E. ...Authors: Chowdhury, R. / Sekirnik, R. / Brissett, N.C. / Krojer, T. / Ho, C.H. / Ng, S.S. / Clifton, I.J. / Ge, W. / Kershaw, N.J. / Fox, G.C. / Muniz, J.R.C. / Vollmar, M. / Phillips, C. / Pilka, E.S. / Kavanagh, K.L. / von Delft, F. / Oppermann, U. / McDonough, M.A. / Doherty, A.J. / Schofield, C.J.
History
DepositionMay 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Data collection / Database references ...Data collection / Database references / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jun 26, 2013Group: Data collection / Derived calculations / Source and taxonomy
Revision 1.3Oct 23, 2013Group: Derived calculations
Revision 1.4Jun 25, 2014Group: Database references
Revision 1.5Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.6Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.7May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: MYC-INDUCED NUCLEAR ANTIGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,47814
Polymers50,4621
Non-polymers1,01613
Water2,666148
1
A: MYC-INDUCED NUCLEAR ANTIGEN
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)308,86784
Polymers302,7746
Non-polymers6,09378
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_666-y+5/4,-x+5/4,-z+5/41
crystal symmetry operation24_666-z+5/4,-y+5/4,-x+5/41
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation19_666-x+5/4,-z+5/4,-y+5/41
Buried area36950 Å2
ΔGint-622.3 kcal/mol
Surface area95550 Å2
MethodPISA
2
A: MYC-INDUCED NUCLEAR ANTIGEN
hetero molecules

A: MYC-INDUCED NUCLEAR ANTIGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,95628
Polymers100,9252
Non-polymers2,03126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation19_666-x+5/4,-z+5/4,-y+5/41
Buried area9650 Å2
ΔGint-168.2 kcal/mol
Surface area34520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.180, 185.180, 185.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-1472-

MN

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Components

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Protein , 1 types, 1 molecules A

#1: Protein MYC-INDUCED NUCLEAR ANTIGEN / FLJ14393 / MINERAL DUST-INDUCED GENE PROTEIN / NUCLEOLAR PROTEIN 52


Mass: 50462.270 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 26-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IUF8

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Non-polymers , 6 types, 161 molecules

#2: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 5.35 Å3/Da / Density % sol: 77 % / Description: NONE
Crystal growDetails: 12% PEG 3350; 0.005M COCL2; 0.005M MGCL2; 0.005M CDCL2; 0.005M NICL2; 0.1M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.56→30 Å / Num. obs: 35135 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Biso Wilson estimate: 68.36 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17
Reflection shellResolution: 2.56→2.7 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2 / % possible all: 97

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Processing

Software
NameVersionClassification
BUSTER-TNT2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.57→29.28 Å / Cor.coef. Fo:Fc: 0.9384 / Cor.coef. Fo:Fc free: 0.9239 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NI MN OGA CD. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=3205. NUMBER WITH APPROX DEFAULT CCP4 ATOM ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NI MN OGA CD. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=3205. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=10. NUMBER TREATED BY BAD NON- BONDED CONTACTS=10
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 1743 5 %RANDOM
Rwork0.1965 ---
obs0.1981 34907 100 %-
Displacement parametersBiso mean: 65.01 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.57→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2990 0 28 148 3166
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d3145HARMONIC2
X-RAY DIFFRACTIONt_angle_deg4276HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1067SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes73HARMONIC2
X-RAY DIFFRACTIONt_gen_planes457HARMONIC5
X-RAY DIFFRACTIONt_it3145HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion406SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3526SEMIHARMONIC4
LS refinement shellResolution: 2.57→2.64 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.4842 135 5.03 %
Rwork0.4432 2547 -
all0.4452 2682 -
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)
14.523-0.45830.02143.6120.97093.1819-0.18930.5442-0.5442-0.35340.15630.34220.43810.0530.033-0.28980.0057-0.03270.0692-0.10260.004686.2664123.06378.8124
20.76190.3923-0.36780-0.11241.2415-0.0036-0.01310.0121-0.00880.00290.01070.0222-0.00140.0007-0.13090.1496-0.09130.16860.15010.066987.4513124.599103.271
35.7801-0.4081-0.30152.105-0.44331.7738-0.2996-0.1408-0.51770.02720.23990.04510.18590.06160.0597-0.23150.1021-0.0356-0.01630.0795-0.02887.9682129.18790.0866
40.2221-0.9783-1.31761.0261.54120.4167-0.0108-0.01520.10150.06180.05650.0374-0.1041-0.0234-0.0456-0.09010.1168-0.03770.10210.00080.303478.9005148.45993.0429
55.36060.7780.81290.3420.11740.4349-0.20950.4982-0.0374-0.11420.2475-0.07940.00350.0764-0.038-0.22590.0578-0.0070.05840.02770.0438100.035137.82387.0104
68.0618-0.12290.12953.4469-2.66161.8459-0.13050.36770.3038-0.0870.0489-0.21050.0359-0.16750.0816-0.2522-0.0507-0.0160.10370.1520.1856120.093151.77782.5481
70.6571-0.2712-1.03533.5945-0.43211.8252-0.03620.0879-0.46070.2541-0.05510.12750.02890.4990.0913-0.30330.13560.0156-0.0059-0.06670.1351108.651124.30885.9207
86.0868-2.9104-1.14424.5533-0.01971.22170.0284-0.10860.5395-0.5442-0.0388-0.5374-0.02020.39070.0104-0.1540.1520.1123-0.0351-0.0572-0.0082119.893115.56278.7276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A 30 - 126
2X-RAY DIFFRACTION2CHAIN A 127 - 131
3X-RAY DIFFRACTION3CHAIN A 132 - 213
4X-RAY DIFFRACTION4CHAIN A 214 - 219
5X-RAY DIFFRACTION5CHAIN A 220 - 296
6X-RAY DIFFRACTION6CHAIN A 297 - 324
7X-RAY DIFFRACTION7CHAIN A 325 - 343
8X-RAY DIFFRACTION8CHAIN A 356 - 465

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