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

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Basic information

Entry
Database: PDB / ID: 4csw
TitleRhodothermus marinus YCFD-like ribosomal protein L16 Arginyl hydroxylase
ComponentsCUPIN 4 FAMILY PROTEIN
KeywordsOXIDOREDUCTASE / 2-OXOGLUTARATE AND IRON DEPENDENT OXYGENASE / DOUBLE STRANDED BETA HELIX FOLD
Function / homology
Function and homology information


2-oxoglutarate-dependent dioxygenase activity / 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. / Jelly Rolls / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / : / Chem-UN9 / Cupin 4 family protein
Similarity search - Component
Biological speciesRHODOTHERMUS MARINUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.821 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 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 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_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 / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5077
Polymers91,6062
Non-polymers9005
Water2,540141
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-57.3 kcal/mol
Surface area33400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.300, 87.690, 90.610
Angle α, β, γ (deg.)90.00, 113.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2063-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9266, -0.0858, -0.3661), (-0.0768, -0.91, 0.4075), (-0.3681, 0.4057, 0.8366)
Vector: -12.6149, 66.2535, -17.3413)

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 146 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-UN9 / N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE


Mass: 280.664 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9ClN2O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 7.5
Details: 0.66MM PROTEIN, 1MM MNCL2, 2MM IOX3, 50%(V/V) TACSIMATE, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2013 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.82→30.21 Å / Num. obs: 27522 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 70.39 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.6
Reflection shellResolution: 2.82→2.89 Å / Redundancy: 5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

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

4ccl


Resolution: 2.821→30.206 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2096 3767 7.2 %
Rwork0.1683 --
obs0.1712 27487 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.28 Å2
Refinement stepCycle: LAST / Resolution: 2.821→30.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6060 0 58 141 6259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036298
X-RAY DIFFRACTIONf_angle_d0.8188628
X-RAY DIFFRACTIONf_dihedral_angle_d16.0632333
X-RAY DIFFRACTIONf_chiral_restr0.03945
X-RAY DIFFRACTIONf_plane_restr0.0051137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8206-2.85630.39161420.32071783X-RAY DIFFRACTION97
2.8563-2.89390.29341410.30311811X-RAY DIFFRACTION97
2.8939-2.93350.37871380.30981817X-RAY DIFFRACTION96
2.9335-2.97540.31641380.28571755X-RAY DIFFRACTION97
2.9754-3.01970.28231450.26811860X-RAY DIFFRACTION97
3.0197-3.06690.28841350.27561738X-RAY DIFFRACTION97
3.0669-3.11710.35491380.2651796X-RAY DIFFRACTION97
3.1171-3.17080.26681410.24931792X-RAY DIFFRACTION97
3.1708-3.22840.27981430.23491833X-RAY DIFFRACTION95
3.2284-3.29040.27571260.22271672X-RAY DIFFRACTION95
3.2904-3.35750.29791450.21321825X-RAY DIFFRACTION96
3.3575-3.43040.28291360.20941711X-RAY DIFFRACTION95
3.4304-3.51010.26151360.19321803X-RAY DIFFRACTION96
3.5101-3.59770.22791350.20141807X-RAY DIFFRACTION95
3.5977-3.69480.28941320.20571719X-RAY DIFFRACTION94
3.6948-3.80340.22171360.17791762X-RAY DIFFRACTION95
3.8034-3.92590.19951420.15151823X-RAY DIFFRACTION96
3.9259-4.06590.18611380.14981729X-RAY DIFFRACTION97
4.0659-4.22820.19341430.14541801X-RAY DIFFRACTION98
4.2282-4.42010.19131420.12551819X-RAY DIFFRACTION98
4.4201-4.65240.1341450.11591856X-RAY DIFFRACTION99
4.6524-4.94270.16151410.11491833X-RAY DIFFRACTION99
4.9427-5.32240.14441420.12221841X-RAY DIFFRACTION99
5.3224-5.85450.18731440.13881809X-RAY DIFFRACTION99
5.8545-6.69360.19221430.1581833X-RAY DIFFRACTION98
6.6936-8.4030.19971390.15231818X-RAY DIFFRACTION99
8.403-30.20750.15051410.13811823X-RAY DIFFRACTION97
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)
11.36260.33150.0390.8242-0.67543.7205-0.0293-0.1238-0.25340.01620.0374-0.0210.31810.12620.00510.45280.0944-0.00080.4957-0.0120.5187.179219.676430.6365
24.3835-0.45980.2751.4157-0.8720.7654-0.03950.43890.2777-0.1542-0.0472-0.0770.13510.10420.11780.5910.00960.04430.4763-0.02690.409-11.769241.84098.7154
33.30160.7741.65532.64561.02021.6738-0.21120.19660.46780.00290.0969-0.4108-0.41880.37430.05620.5241-0.0871-0.02820.6066-0.02350.661417.867748.257822.1452
42.39230.484-0.57013.51750.49382.2367-0.0842-0.21140.56540.2725-0.05850.4768-0.39190.04030.12880.60150.0904-0.06080.5447-0.03940.7007-33.716461.632813.933
52.8894-1.45890.46851.5284-0.09670.1505-0.0537-0.1696-0.1033-0.04860.11980.0657-0.05440.1234-0.04740.51320.00070.02170.653-0.03130.5061-8.017836.485911.2779
63.40251.0444-1.19972.2189-1.24423.2069-0.07360.0367-0.1413-0.12870.03260.06210.5077-0.3350.02750.6057-0.03740.01830.5122-0.04040.4863-37.57831.207414.4786
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2 THROUGH 228 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 229 THROUGH 290 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 291 THROUGH 389 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 2 THROUGH 203 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 204 THROUGH 266 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 267 THROUGH 389 )

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