[English] 日本語
Yorodumi
- PDB-4lit: Structure of YcfD a Ribosomal oxygenase from Escherichia coli in ... -

+
Open data


ID or keywords:

Loading...

-
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 hydroxylaseRibosome
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

#1: Protein 50S ribosomal protein L16 arginine hydroxylase / Ribosome / 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 / Α-Ketoglutaric acid


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


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more