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- PDB-4nub: Crystal structure of Escherichia coli ribosomal oxygenase YcfD -

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Basic information

Entry
Database: PDB / ID: 4nub
TitleCrystal structure of Escherichia coli ribosomal oxygenase YcfD
Components50S ribosomal protein L16 arginine hydroxylaseRibosome
KeywordsOXIDOREDUCTASE / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / jelly roll / cupin / beta-barrel / 2OG/Fe2+ dependent oxygenase / Ribosomal protein L-16
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
: / Ribosomal protein uL16 3-hydroxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsVan staalduinen, L.M. / Jia, Z. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structure and Functional Analysis of YcfD, a Novel 2-Oxoglutarate/Fe(2+)-Dependent Oxygenase Involved in Translational Regulation in Escherichia coli.
Authors: van Staalduinen, L.M. / Novakowski, S.K. / Jia, Z.
History
DepositionDec 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 50S ribosomal protein L16 arginine hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4823
Polymers44,3341
Non-polymers1482
Water91951
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)88,9646
Polymers88,6682
Non-polymers2964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area6570 Å2
ΔGint-72 kcal/mol
Surface area31550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.731, 75.731, 210.898
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Detailsbiological assembly is a dimer generated from the monomer in the asymmetric unit by the operation -y,-x,-z+1/2

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Components

#1: Protein 50S ribosomal protein L16 arginine hydroxylase / Ribosome / Ribosomal oxygenase YcfD / ROX


Mass: 44333.980 Da / Num. of mol.: 1 / Mutation: E146A, K147A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1128, JW1114, ycfD / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 DE3
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-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 3.41 Å3/Da / Density % sol: 63.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 3.6% PEG 4000, 30% Glycerol, 0.07M sodium acetate, 0.5 uL of 1/10 dilution of seed solution, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97913, 0.97927, 0.91837
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 9, 2009 / Details: mirrors
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979131
20.979271
30.918371
ReflectionResolution: 2.7→20 Å / Num. all: 31993 / Num. obs: 31993 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHARPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→19.926 Å / SU ML: 0.39 / σ(F): 1.44 / Phase error: 22.31 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 893 5.07 %Random
Rwork0.1781 ---
all0.1806 17671 --
obs0.1806 17602 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→19.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2872 0 7 51 2930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092977
X-RAY DIFFRACTIONf_angle_d1.2184056
X-RAY DIFFRACTIONf_dihedral_angle_d15.4411089
X-RAY DIFFRACTIONf_chiral_restr0.086418
X-RAY DIFFRACTIONf_plane_restr0.006541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.86880.38781700.30752681X-RAY DIFFRACTION100
2.8688-3.08950.29741490.25982712X-RAY DIFFRACTION100
3.0895-3.39910.24441530.20352740X-RAY DIFFRACTION100
3.3991-3.88770.23521530.17832752X-RAY DIFFRACTION100
3.8877-4.88620.1831250.142845X-RAY DIFFRACTION100
4.8862-19.92660.19641430.15942979X-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)
10.15480.0213-0.06310.38240.07130.60560.00680.01690.00960.08530.1747-0.0775-0.0689-0.46770.0670.15660.08220.02060.22720.03720.17733.913314.926584.3808
20.2007-0.11250.33710.0113-0.06430.2468-0.02350.0616-0.0254-0.05840.28240.108-0.17990.13050.09170.2324-0.1426-0.01380.2259-0.01290.2210.6204-0.965157.1806
30.13320.11310.01880.1787-0.05380.1563-0.13790.2331-0.0599-0.14470.2893-0.08120.1023-0.24150.2413-0.0802-0.3670.03670.0140.05180.205516.071324.290458.7946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 181 )
2X-RAY DIFFRACTION2chain 'A' and (resid 182 through 259 )
3X-RAY DIFFRACTION3chain 'A' and (resid 260 through 372 )

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