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- PDB-4cug: Rhodothermus marinus YCFD-like ribosomal protein L16 Arginyl hydr... -

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Basic information

Entry
Database: PDB / ID: 4cug
TitleRhodothermus marinus YCFD-like ribosomal protein L16 Arginyl hydroxylase in complex substrate fragment
Components
  • 50S RIBOSOMAL PROTEIN L16
  • CUPIN 4 FAMILY PROTEIN
KeywordsTRANSLATION / 2-OXOGLUTARATE AND IRON DEPENDENT OXYGENASE / DOUBLE STRANDED BETA HELIX FOLD
Function / homology
Function and homology information


2-oxoglutarate-dependent dioxygenase activity / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation / metal ion binding
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. / Ribosomal protein L16 signature 1. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L16 / : / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Jelly Rolls / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / N-OXALYLGLYCINE / PHOSPHATE ION / Large ribosomal subunit protein uL16 / Cupin 4 family protein
Similarity search - Component
Biological speciesRHODOTHERMUS MARINUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsMcDonough, M.A. / Sekirnik, R. / 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
DepositionMar 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 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 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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.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_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_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: CUPIN 4 FAMILY PROTEIN
B: CUPIN 4 FAMILY PROTEIN
E: 50S RIBOSOMAL PROTEIN L16
F: 50S RIBOSOMAL PROTEIN L16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,60711
Polymers95,8714
Non-polymers7357
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11340 Å2
ΔGint-85.1 kcal/mol
Surface area32410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.220, 117.470, 120.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.998, 0.013, -0.0611), (-0.062, -0.3197, 0.9455), (-0.0072, 0.9474, 0.3199)
Vector: 68.486, 80.1631, -55.5864)

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABEF

#1: Protein CUPIN 4 FAMILY PROTEIN / RIBOSOMAL PROTEIN L16 ARGINYL HYDROXYLASE


Mass: 45803.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOTHERMUS MARINUS (bacteria) / Strain: DSM 4252 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: D0MK34
#2: Protein/peptide 50S RIBOSOMAL PROTEIN L16 / RPL16


Mass: 2132.568 Da / Num. of mol.: 2 / Fragment: RESIDUES 72-91 / Source method: obtained synthetically / Source: (synth.) RHODOTHERMUS MARINUS (bacteria) / References: UniProt: D0MGW1

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Non-polymers , 4 types, 7 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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Details

Sequence detailsA FRAGEMENT (RESIDUES 72-91) OF THE FULL LENGTH SEQUENCE WAS USED FOR CO-CRYSTALLISATION

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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: 3.89 Å3/Da / Density % sol: 68.41 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1M TRIS-HCL PH8.5, 1MM MNCL2, 1MM OGA, 2MM L16 PEPTIDE, 0.66MM PROTEIN, 0.1M AMMONIUM DIHYDROGEN PHOSPHATE, 45% (V/V) METHYL-2-4-PENTANEDIOL, ROOM TEMPERATURE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.0073
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2012 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0073 Å / Relative weight: 1
ReflectionResolution: 2.96→58.74 Å / Num. obs: 29641 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 97.22 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.4
Reflection shellResolution: 2.96→3.04 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CCL

4ccl


Resolution: 2.96→58.74 Å / SU ML: 0.39 / σ(F): 1.49 / Phase error: 24.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 2001 6.8 %
Rwork0.2101 --
obs0.2112 29585 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 1.898 Å2 / ksol: 1.035 e/Å3
Displacement parametersBiso mean: 106.55 Å2
Refinement stepCycle: LAST / Resolution: 2.96→58.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6219 0 43 0 6262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036448
X-RAY DIFFRACTIONf_angle_d0.7758819
X-RAY DIFFRACTIONf_dihedral_angle_d14.7532419
X-RAY DIFFRACTIONf_chiral_restr0.031962
X-RAY DIFFRACTIONf_plane_restr0.0051168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9615-3.03550.35621360.33461938X-RAY DIFFRACTION100
3.0355-3.11760.35271470.3241935X-RAY DIFFRACTION100
3.1176-3.20930.30791420.2961921X-RAY DIFFRACTION100
3.2093-3.31290.30031340.2811970X-RAY DIFFRACTION100
3.3129-3.43130.27651390.26431953X-RAY DIFFRACTION100
3.4313-3.56870.23141430.24571943X-RAY DIFFRACTION100
3.5687-3.73110.27321420.24341956X-RAY DIFFRACTION100
3.7311-3.92770.25681470.22711956X-RAY DIFFRACTION100
3.9277-4.17370.24961420.21361937X-RAY DIFFRACTION100
4.1737-4.49590.20061400.18831976X-RAY DIFFRACTION100
4.4959-4.94810.19911470.1851981X-RAY DIFFRACTION100
4.9481-5.66360.23311430.19151992X-RAY DIFFRACTION100
5.6636-7.13360.21121480.22012010X-RAY DIFFRACTION100
7.1336-58.74650.18531510.1692116X-RAY DIFFRACTION100
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)
15.41320.4641-2.88163.08290.80157.7014-0.5099-0.5474-0.29760.23070.20140.33290.3340.1530.25230.63680.0569-0.03670.50240.07760.573529.0119114.2253129.0199
21.8688-1.0119-1.06894.2038-1.0772.69270.0672-0.07590.31660.1944-0.167-0.5572-0.2370.23470.10180.5944-0.00950.08420.5681-0.09020.586139.36130.6513105.1435
33.54040.78670.6913.7382-0.40797.23610.0521-0.32810.21170.24230.1318-1.40840.51521.8443-0.00660.58640.0971-0.04560.863-0.08410.942356.9554120.7223114.5852
43.5451.4752-0.4044.73062.02655.03220.28180.2671.014-0.6191-0.2951-0.4816-0.90190.0705-0.01460.96930.16180.24540.71050.16081.075335.6927162.938393.6634
51.657-1.08890.4653.6231-0.49332.40340.24820.01110.1825-0.1561-0.18640.7218-0.315-0.7861-0.06410.61190.06440.09390.9007-0.12550.649618.8022142.375697.4703
60.7681-2.2184-0.16368.9521-1.75931.960.43170.69230.54680.4582-0.51241.2128-0.77320.21680.05071.38080.23160.18951.26790.13561.242726.115124.3922122.7765
72.8691.7174-1.96995.79041.29227.21610.5811-0.65270.10340.71280.2669-0.13410.4531.1545-0.85391.5116-0.0598-0.0241.4829-0.02591.141938.7406153.7919101.781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2 THROUGH 203 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 204 THROUGH 306 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 307 THROUGH 389 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 2 THROUGH 195 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 196 THROUGH 388 )
6X-RAY DIFFRACTION6CHAIN E AND (RESID 78 THROUGH 85 )
7X-RAY DIFFRACTION7CHAIN F AND (RESID 77 THROUGH 85 )

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