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- PDB-4diq: Crystal Structure of human NO66 -

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Entry
Database: PDB / ID: 4diq
TitleCrystal Structure of human NO66
ComponentsLysine-specific demethylase NO66
KeywordsOXIDOREDUCTASE / Structural Genomics / Structural Genomics Consortium / SGC / histone demethylase
Function / homology
Function and homology information


protein-L-histidine (3S)-3-hydroxylase / protein demethylase activity / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / peptidyl-histidine dioxygenase activity / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / histone H3K36 demethylase activity / histone H3K4 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / Protein hydroxylation ...protein-L-histidine (3S)-3-hydroxylase / protein demethylase activity / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / peptidyl-histidine dioxygenase activity / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / histone H3K36 demethylase activity / histone H3K4 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / Protein hydroxylation / negative regulation of osteoblast differentiation / iron ion binding / negative regulation of DNA-templated transcription / nucleolus / nucleoplasm / nucleus
Similarity search - Function
: / Ribosomal oxygenase 1, C-terminal winged helix domain / 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. ...: / Ribosomal oxygenase 1, C-terminal winged helix domain / 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 / PYRIDINE-2,4-DICARBOXYLIC ACID / Ribosomal oxygenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsVollmar, M. / Krojer, T. / Ng, S. / Pilka, E. / Bray, J. / Pike, A.C.W. / Filippakopoulos, P. / Roos, A. / Arrowsmith, C.H. / Edwards, E. ...Vollmar, M. / Krojer, T. / Ng, S. / Pilka, E. / Bray, J. / Pike, A.C.W. / Filippakopoulos, P. / Roos, A. / Arrowsmith, C.H. / Edwards, E. / Bountra, C. / von Delft, F. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of human NO66
Authors: Vollmar, M. / Krojer, T. / Stan, N.G. / Pilka, E. / Phillips, C. / Burgess-Brown, N. / Bray, J. / Pike, A.C.W. / Filippakopoulos, P. / Roos, A. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. ...Authors: Vollmar, M. / Krojer, T. / Stan, N.G. / Pilka, E. / Phillips, C. / Burgess-Brown, N. / Bray, J. / Pike, A.C.W. / Filippakopoulos, P. / Roos, A. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Oppermann, U.
History
DepositionJan 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysine-specific demethylase NO66
B: Lysine-specific demethylase NO66
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,8937
Polymers111,3462
Non-polymers5485
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-87 kcal/mol
Surface area38670 Å2
MethodPISA
2
A: Lysine-specific demethylase NO66
B: Lysine-specific demethylase NO66
hetero molecules

A: Lysine-specific demethylase NO66
B: Lysine-specific demethylase NO66
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,78714
Polymers222,6914
Non-polymers1,09510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
Buried area20280 Å2
ΔGint-192 kcal/mol
Surface area72770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.674, 149.550, 105.311
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Lysine-specific demethylase NO66 / Nucleolar protein 66 / hsNO66


Mass: 55672.785 Da / Num. of mol.: 2 / Fragment: UNP residues 161-641
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NO66, C14orf169 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H6W3, [histone H3]-dimethyl-L-lysine36 demethylase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-PD2 / PYRIDINE-2,4-DICARBOXYLIC ACID


Mass: 167.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05M (NH4)2SO4, 0.05M BIS-TRIS pH 6.5, 30% pentaerythritol ethoxylate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9919 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 49295 / Num. obs: 49295 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rsym value: 0.076 / Net I/σ(I): 22.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4801 / % possible all: 98.6

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Processing

Software
NameVersionClassification
notapplicabledata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.46 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 15.08 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / ESU R: 0.292 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23045 1986 4 %RANDOM
Rwork0.18497 ---
all0.18702 47243 --
obs0.18702 47243 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.577 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20 Å2
2---2.49 Å20 Å2
3---3.38 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7228 0 31 120 7379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197482
X-RAY DIFFRACTIONr_bond_other_d0.0050.025095
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.9710197
X-RAY DIFFRACTIONr_angle_other_deg1.157312302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3185922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.14422.778360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.052151167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8671572
X-RAY DIFFRACTIONr_chiral_restr0.0890.21110
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218425
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021629
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 77 -
Rwork0.315 3208 -
obs--97.94 %
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)
10.7155-0.23890.27920.4151-0.44870.668-0.10930.0548-0.03810.14660.0383-0.0941-0.12010.05530.0710.2609-0.032-0.10460.1716-0.05340.1278-27.1936-53.4014-5.8933
20.0463-0.04740.05660.16680.07310.28030.0198-0.02410.00480.00950.05170.0048-0.024-0.0038-0.07140.20480.00950.01980.1955-0.01260.208-47.3152-47.1981-33.0685
31.76163.01490.43745.52531.67182.47280.2562-0.38450.07380.3589-0.50580.18920.01440.29280.24960.37530.0180.1610.21070.10120.1405-59.9695-73.55726.6525
40.37890.62010.21081.10090.31570.3730.0518-0.00920.02670.01050.11410.1238-0.0937-0.1236-0.1660.17450.02940.04060.2560.14660.2006-64.1969-63.2356-8.0664
50.4650.2092-0.2350.78640.34230.4157-0.0731-0.0554-0.0157-0.1516-0.02450.1926-0.04080.03790.09760.10690.0161-0.06390.16160.00370.3062-62.2662-65.3541-65.3305
60.034-0.06780.14870.2495-0.4071.3797-0.01110.0234-0.03170.07360.09720.0122-0.25-0.06-0.0860.22960.0232-0.00070.2143-0.04190.1586-48.8181-43.7571-30.0164
70.9098-0.531-0.49020.4664-0.0120.87260.0556-0.05760.0399-0.1046-0.03040.02270.15630.1149-0.02530.2086-0.04130.03260.2143-0.05480.2027-29.166-59.9417-71.7381
81.1771.1693-0.28211.268-0.12820.3884-0.0045-0.0502-0.191-0.0336-0.0021-0.1636-0.10540.01140.00660.1607-0.02560.00560.1809-0.01940.2443-27.418-50.7951-63.3269
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A181 - 360
2X-RAY DIFFRACTION2A361 - 465
3X-RAY DIFFRACTION3A466 - 489
4X-RAY DIFFRACTION4A490 - 591
5X-RAY DIFFRACTION5B181 - 374
6X-RAY DIFFRACTION6B375 - 451
7X-RAY DIFFRACTION7B452 - 492
8X-RAY DIFFRACTION8B493 - 589

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