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- PDB-4ccl: X-Ray structure of E. coli ycfD -

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Basic information

Entry
Database: PDB / ID: 4ccl
TitleX-Ray structure of E. coli ycfD
Components50S RIBOSOMAL PROTEIN L16 ARGININE HYDROXYLASE
KeywordsOXIDOREDUCTASE / 2OG AND IRON DEPENDENT OXYGENASE
Function / homology
Function and homology information


[50S ribosomal protein L16]-arginine 3-hydroxylase / histone H3K36 demethylase activity / histone H3K4 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / post-translational protein modification / ferrous iron binding / protein homodimerization activity
Similarity search - Function
50S ribosomal protein L16 arginine hydroxylase; Chain A, Domain 2 / ROXA-like, winged helix / ROXA-like winged helix / JmjC domain-containing / JmjC domain / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Cupin / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. ...50S ribosomal protein L16 arginine hydroxylase; Chain A, Domain 2 / ROXA-like, winged helix / ROXA-like winged helix / JmjC domain-containing / JmjC domain / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Cupin / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Ribosomal protein uL16 3-hydroxylase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.596 Å
AuthorsMcDonough, M.A. / Ho, C.H. / Kershaw, N.J. / Schofield, C.J.
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
DepositionOct 23, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2May 21, 2014Group: Database references
Revision 1.3Jun 25, 2014Group: Database references
Revision 1.4Feb 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 1.5Oct 16, 2019Group: Data collection / Derived calculations / Other / Category: pdbx_database_status / reflns_shell / struct_conn
Item: _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Jun 3, 2020Group: Derived calculations
Category: pdbx_struct_conn_angle / pdbx_struct_sheet_hbond ...pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _struct_conf.pdbx_PDB_helix_id / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 50S RIBOSOMAL PROTEIN L16 ARGININE HYDROXYLASE
B: 50S RIBOSOMAL PROTEIN L16 ARGININE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,26815
Polymers86,1832
Non-polymers1,08413
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-188.6 kcal/mol
Surface area32490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.693, 120.693, 133.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein 50S RIBOSOMAL PROTEIN L16 ARGININE HYDROXYLASE / RIBOSOMAL OXYGENASE YCFD / ROX


Mass: 43091.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P27431, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1M TRIS.HCL PH 8.5, 0.2M LITHIUM SULPHATE, 1.26 M AMMONIUM SULFATE, 0.001 M FECL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 4, 2009 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.6→44.8 Å / Num. obs: 31066 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 68.23 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.596→41.765 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 27.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 2000 6.4 %
Rwork0.1983 --
obs0.2016 31048 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.596→41.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5877 0 49 155 6081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046105
X-RAY DIFFRACTIONf_angle_d1.078334
X-RAY DIFFRACTIONf_dihedral_angle_d16.6122211
X-RAY DIFFRACTIONf_chiral_restr0.08856
X-RAY DIFFRACTIONf_plane_restr0.0061113
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5964-2.66130.44351380.37291997X-RAY DIFFRACTION98
2.6613-2.73330.41191410.31232043X-RAY DIFFRACTION100
2.7333-2.81370.34341400.29552054X-RAY DIFFRACTION100
2.8137-2.90450.35231410.26322043X-RAY DIFFRACTION100
2.9045-3.00830.3261400.25462035X-RAY DIFFRACTION100
3.0083-3.12870.29371400.25482040X-RAY DIFFRACTION100
3.1287-3.2710.29791430.26292068X-RAY DIFFRACTION100
3.271-3.44340.29921410.21992054X-RAY DIFFRACTION100
3.4434-3.6590.31411430.20442076X-RAY DIFFRACTION100
3.659-3.94130.24071420.18092064X-RAY DIFFRACTION100
3.9413-4.33760.2081440.15912094X-RAY DIFFRACTION100
4.3376-4.96430.18531450.13982105X-RAY DIFFRACTION100
4.9643-6.25120.22121470.18132133X-RAY DIFFRACTION100
6.2512-41.770.21181550.18952242X-RAY DIFFRACTION99
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)
12.6341-0.45750.58623.4786-0.26991.43740.1678-0.51230.8415-0.02-0.23890.1954-0.169-0.50870.02770.54470.2869-0.05070.9444-0.21390.749238.550229.069244.6246
22.02011.2830.53233.8004-0.36790.9509-0.0601-0.38510.89530.7775-0.3413-1.2125-0.52960.43610.18790.72430.1137-0.2790.9702-0.15741.361557.88539.029152.6095
32.8609-0.24271.41142.90920.55563.2642-0.0232-0.44531.11360.0841-0.2528-0.5235-0.24440.29340.27450.52170.1972-0.01540.7414-0.12020.903246.646230.016445.4412
41.7852-1.0677-0.38042.34550.1845-0.0726-0.42180.42590.03511.25890.4371-0.89870.5842-0.4676-0.13011.21430.05290.06671.0870.1191.236158.228428.802828.7895
52.09140.28520.32442.2122-0.53391.6074-0.05660.22481.4589-0.1085-0.4522-0.6998-0.46350.46910.36470.60960.2593-0.0550.76450.02141.14645.094535.356439.5554
62.48-1.5731-1.70372.17130.67730.2096-0.0960.1116-0.1637-0.00210.08950.2599-0.1904-0.2463-0.06890.59610.295-0.13370.7956-0.12940.514669.6414-3.153236.5398
74.2687-1.03020.18412.5748-0.15762.3815-0.1525-1.2974-0.20520.53180.02120.3320.2032-0.14570.15920.6950.29180.09421.23630.1180.559747.15168.758562.7562
82.5661-1.04870.77332.9153-0.7462.81540.00220.3877-0.3505-0.0522-0.1518-0.36680.06910.52250.10140.42630.1807-0.03510.5911-0.01090.482795.8238-19.493235.0365
90.60790.1457-0.00351.8514-1.08954.614-0.0418-0.4526-0.03410.917-0.2814-0.4703-0.96490.71860.18871.09580.0949-0.42270.8767-0.03610.7557100.9239-6.169253.619
101.4483-0.50221.12562.7619-0.40312.1397-0.3009-0.21810.17320.4638-0.0874-0.2556-0.63350.21590.42590.51570.1451-0.10880.57710.00150.450194.0509-14.344441.0462
112.946-0.74550.54373.2011.3582.8668-0.3402-0.85760.50341.5605-0.07390.4030.0243-0.67060.38541.2240.06910.08760.8551-0.15390.736683.6914-17.11956.7201
121.7104-0.4394-0.24212.1318-0.28892.1536-0.2288-0.2808-0.32630.4718-0.0331-0.4174-0.03980.24370.18770.45380.1654-0.04880.51910.02410.437194.7756-21.50345.3696
131.8762-2.0841-0.44021.70060.27970.10890.34170.14050.0255-0.2124-0.22550.11570.1062-0.1028-0.06810.76220.3267-0.08870.7518-0.08440.537758.50366.557138.3045
143.38050.8294-1.77613.6081-1.16433.6329-0.30140.22390.11620.17750.1523-0.204-0.2298-0.06660.11230.70970.1696-0.05070.51560.00560.435790.85475.745422.7067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:44)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 45:89)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 90:144)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 145:166)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 167:202)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 203:259)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 260:372)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 1:44)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 45:89)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 90:144)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 145:166)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 167:202)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 203:259)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 260:372)

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