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- PDB-4lit: Structure of YcfD a Ribosomal oxygenase from Escherichia coli in ... -

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Basic information

Entry
Database: PDB / ID: 4lit
TitleStructure of YcfD a Ribosomal oxygenase from Escherichia coli in complex with Cobalt and 2-oxoglutarate.
Components50S ribosomal protein L16 arginine hydroxylase
KeywordsOXIDOREDUCTASE / JmjC Domain / Dioxygenase / Hydroxylation
Function / homology
Function and homology information


[50S ribosomal protein L16]-arginine 3-hydroxylase / 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
2-OXOGLUTARIC ACID / : / Ribosomal protein uL16 3-hydroxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsBrissett, N.C. / Doherty, A.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. / Vollmar, M. / Phillips, C. / Pilka, E.S. ...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. / 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
DepositionJul 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Jul 9, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_ref_seq_dif.details / _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: 50S ribosomal protein L16 arginine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3833
Polymers46,1781
Non-polymers2052
Water2,468137
1
A: 50S ribosomal protein L16 arginine hydroxylase
hetero molecules

A: 50S ribosomal protein L16 arginine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7656
Polymers92,3552
Non-polymers4104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7030 Å2
ΔGint-72 kcal/mol
Surface area31380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.140, 74.140, 208.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 46177.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1128, JW1114, ycfD / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834s
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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 3.11 Å3/Da / Density % sol: 60.42 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 10mM Cobalt chloride, 50mM 2-oxoglutarate pH 4.2, 1.5M 1,6 Hexanediol, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 18, 2012 / Details: mirrors
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→69.869 Å / Num. all: 23748 / Num. obs: 23748 / % possible obs: 100 % / Redundancy: 12.9 % / Rsym value: 0.164 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.5312.60.731.14227133610.73100
2.53-2.6813.70.6121.34418632180.612100
2.68-2.8713.40.4181.84053030210.418100
2.87-3.1130.3072.43692328390.307100
3.1-3.3912.70.1893.73331926200.189100
3.39-3.7912.50.1384.82968423740.138100
3.79-4.3812.40.1035.82656521490.103100
4.38-5.3712.80.08372338518270.083100
5.37-7.5912.80.0976.31869314610.097100
7.59-33.15611.10.0578.297828780.05799

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.64 Å33.16 Å
Translation5.64 Å33.16 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.21data scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
PHENIX1.8.2_1309refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LIU

4liu


Resolution: 2.4→33.156 Å / Occupancy max: 1 / Occupancy min: 0.44 / SU ML: 0.28 / σ(F): 0.41 / Phase error: 22.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 2240 5.15 %
Rwork0.1838 --
obs0.1864 43461 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.87 Å2 / Biso mean: 44.6695 Å2 / Biso min: 20.57 Å2
Refinement stepCycle: LAST / Resolution: 2.4→33.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 11 137 3034
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)
13.59831.3514-0.15083.61240.20393.3901-0.0425-0.00770.1277-0.09770.10360.0683-0.12-0.0112-0.06960.28480.0350.00770.2327-0.01860.237526.097951.551772.9587
23.2642-0.28-1.06653.43420.23054.39750.0452-0.19790.496-0.21230.1703-0.6311-0.3141.0927-0.19980.3682-0.11410.05030.4967-0.03730.387344.097257.970473.7943
35.54862.8778-0.7424.1209-2.83032.39140.0143-0.08720.37260.5471-0.21650.0986-0.6633-0.15870.10940.36840.0806-0.00490.2737-0.03590.252122.014950.017682.9415
43.6331.4928-0.62393.15780.86574.8175-0.14280.1808-0.1793-0.06860.1952-0.20810.18360.4826-0.03660.27730.02390.02810.28850.00150.282335.209746.120569.9054
50.4195-0.80441.02091.3647-2.05963.7134-0.0222-0.11640.0170.08150.1359-0.0592-0.1071-0.2293-0.11570.25330.0159-0.04070.30590.00050.281136.389831.2621110.7328
62.1562-1.29110.49172.55010.26151.7788-0.2103-0.3504-0.10220.23450.3597-0.00540.14710.2103-0.13780.40350.08940.01940.3454-0.02920.298224.571658.820497.6663
73.0869-2.4467-1.35742.32740.03193.34250.0462-0.1358-0.1647-0.034-0.01370.21520.2716-0.20260.10040.3579-0.0414-0.02060.2458-0.04690.354115.986357.964797.988
82.5279-0.2191-0.07951.4240.85842.6540.1436-0.0086-0.01880.1202-0.02350.00770.17370.093-0.08750.33270.0367-0.00940.2539-0.0260.275517.969666.273999.2486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 36:83)A36 - 83
2X-RAY DIFFRACTION2(chain A and resid 84:129)A84 - 129
3X-RAY DIFFRACTION3(chain A and resid 130:141)A130 - 141
4X-RAY DIFFRACTION4(chain A and resid 142:236)A142 - 236
5X-RAY DIFFRACTION5(chain A and resid 237:293)A237 - 293
6X-RAY DIFFRACTION6(chain A and resid 294:355)A294 - 355
7X-RAY DIFFRACTION7(chain A and resid 356:378)A356 - 378
8X-RAY DIFFRACTION8(chain A and resid 379:407)A379 - 407

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