[English] 日本語
Yorodumi
- PDB-4xet: Fe-Cl bound Y157F CDO at pH ~7.0 in the presence of azide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xet
TitleFe-Cl bound Y157F CDO at pH ~7.0 in the presence of azide
ComponentsCysteine dioxygenase type 1
KeywordsOXIDOREDUCTASE / Cupin Fold / cysteine to cysteine sulfinic acid catalysis / Cytosol / thiol dioxygenase
Function / homology
Function and homology information


L-cysteine metabolic process / Degradation of cysteine and homocysteine / taurine biosynthetic process / cysteine dioxygenase / cysteine dioxygenase activity / L-cysteine catabolic process / cysteine metabolic process / response to glucagon / nickel cation binding / response to amino acid ...L-cysteine metabolic process / Degradation of cysteine and homocysteine / taurine biosynthetic process / cysteine dioxygenase / cysteine dioxygenase activity / L-cysteine catabolic process / cysteine metabolic process / response to glucagon / nickel cation binding / response to amino acid / response to glucocorticoid / response to cAMP / response to organonitrogen compound / lactation / ferrous iron binding / response to ethanol / zinc ion binding / cytosol
Similarity search - Function
Cysteine dioxygenase type I / Cysteine dioxygenase type I / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Cysteine dioxygenase type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.3 Å
AuthorsDriggers, C.M. / Karplus, P.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)NIH-DK-056649 United States
Department of Energy (DOE, United States)DE-AC02-98CH10886 United States
CitationJournal: J. Mol. Biol. / Year: 2016
Title: Structure-Based Insights into the Role of the Cys-Tyr Crosslink and Inhibitor Recognition by Mammalian Cysteine Dioxygenase.
Authors: Driggers, C.M. / Kean, K.M. / Hirschberger, L.L. / Cooley, R.B. / Stipanuk, M.H. / Karplus, P.A.
History
DepositionDec 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cysteine dioxygenase type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1343
Polymers23,0431
Non-polymers912
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-31 kcal/mol
Surface area9380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.600, 57.600, 122.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-858-

HOH

-
Components

#1: Protein Cysteine dioxygenase type 1 / Cysteine dioxygenase type I / CDO-I


Mass: 23042.889 Da / Num. of mol.: 1 / Mutation: Y157F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cdo1 / Production host: Escherichia coli (E. coli) / References: UniProt: P21816, cysteine dioxygenase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Purified enzyme was concentrated to ~8 mg/mL and then added into a crystallization screen containing 0.1 M tri-sodium citrate pH=5.6, 24-34% PEG 4K, and 0.1-0.25 M ammonium acetate. 1.5L of ...Details: Purified enzyme was concentrated to ~8 mg/mL and then added into a crystallization screen containing 0.1 M tri-sodium citrate pH=5.6, 24-34% PEG 4K, and 0.1-0.25 M ammonium acetate. 1.5L of protein solution was added to each well and mixed with an equivalent volume of reservoir solution., pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
PH range: 6.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2013
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→34 Å / Num. all: 47533 / Num. obs: 47060 / % possible obs: 91 % / Redundancy: 40.7 % / Net I/σ(I): 27.8
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 18 % / Mean I/σ(I) obs: 1.5 / % possible all: 52

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIX(phenix.refine: 1.9_1692)phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4IEU with Cys removed

4ieu


Resolution: 1.3→33.907 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1885 4574 9.72 %same 5% as 4IEU
Rwork0.1628 ---
obs0.1653 47060 91.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→33.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1509 0 2 289 1800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011655
X-RAY DIFFRACTIONf_angle_d1.0112254
X-RAY DIFFRACTIONf_dihedral_angle_d13.184629
X-RAY DIFFRACTIONf_chiral_restr0.083241
X-RAY DIFFRACTIONf_plane_restr0.006297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.2851830.2777823X-RAY DIFFRACTION52
1.3148-1.33030.3155840.2886854X-RAY DIFFRACTION56
1.3303-1.34650.3123910.2668944X-RAY DIFFRACTION62
1.3465-1.36350.27191180.23781002X-RAY DIFFRACTION67
1.3635-1.38150.24641010.23081088X-RAY DIFFRACTION71
1.3815-1.40040.26191290.22821186X-RAY DIFFRACTION77
1.4004-1.42040.20691230.22571322X-RAY DIFFRACTION87
1.4204-1.44160.22341630.22771481X-RAY DIFFRACTION95
1.4416-1.46420.24241580.20551453X-RAY DIFFRACTION97
1.4642-1.48820.22221570.18611494X-RAY DIFFRACTION97
1.4882-1.51380.21161730.17661511X-RAY DIFFRACTION98
1.5138-1.54130.21681460.17351476X-RAY DIFFRACTION98
1.5413-1.5710.19771780.16521500X-RAY DIFFRACTION98
1.571-1.60310.18751780.16261475X-RAY DIFFRACTION98
1.6031-1.63790.17381490.16941519X-RAY DIFFRACTION98
1.6379-1.6760.19381790.15651480X-RAY DIFFRACTION98
1.676-1.71790.17161720.16331502X-RAY DIFFRACTION98
1.7179-1.76440.19471580.17031519X-RAY DIFFRACTION98
1.7644-1.81630.20471540.16651535X-RAY DIFFRACTION98
1.8163-1.87490.19331580.16261528X-RAY DIFFRACTION98
1.8749-1.94190.18481500.16061546X-RAY DIFFRACTION99
1.9419-2.01970.18151800.15921523X-RAY DIFFRACTION99
2.0197-2.11160.1831810.15591524X-RAY DIFFRACTION99
2.1116-2.22290.17541540.15441569X-RAY DIFFRACTION99
2.2229-2.36210.1821650.14991536X-RAY DIFFRACTION99
2.3621-2.54440.17261620.16311590X-RAY DIFFRACTION100
2.5444-2.80040.21221850.16471554X-RAY DIFFRACTION99
2.8004-3.20530.1971820.16371594X-RAY DIFFRACTION100
3.2053-4.03730.18891750.1441613X-RAY DIFFRACTION100
4.0373-33.91840.14881880.14631745X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.2187 Å / Origin y: 2.993 Å / Origin z: -49.6165 Å
111213212223313233
T0.0556 Å2-0.0002 Å20.0002 Å2-0.0733 Å20.0018 Å2--0.0665 Å2
L0.5904 °20.3551 °2-0.1597 °2-0.5658 °20.0474 °2--0.5765 °2
S0.0213 Å °-0.0115 Å °-0.0239 Å °0.0421 Å °-0.0072 Å °-0.0091 Å °0.0309 Å °-0.0158 Å °0.0719 Å °
Refinement TLS groupSelection details: chain 'A' and resid 5 through 190

+
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://pdbjlvh1.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