[English] 日本語
Yorodumi
- PDB-4xfg: cysteine dioxygenase variant - C93A at pH 6.2 with cysteine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xfg
Titlecysteine dioxygenase variant - C93A at pH 6.2 with cysteine
ComponentsCysteine dioxygenase type 1
KeywordsOXIDOREDUCTASE / Cupin Fold / cysteine to cysteine sulfinic acid catalysis / 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 / : / Cysteine dioxygenase type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.401 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 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Sep 20, 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 ...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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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

-
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)23,2394
Polymers23,0271
Non-polymers2123
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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-698-

HOH

-
Components

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


Mass: 23026.822 Da / Num. of mol.: 1 / Mutation: C93A
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 / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1M tri-sodium citrate pH=5.6, 24% PEG 4000, 0.15M ammonium acetate. 1:1 drop ratio with microseeding.; Soak solution at pH 6.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2014
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.4→34 Å / Num. all: 41405 / Num. obs: 41323 / % possible obs: 100 % / Redundancy: 23.7 % / Net I/σ(I): 11.3
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 0.8 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4ieu

4ieu


Resolution: 1.401→33.907 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1965 4073 9.86 %same 5% as 4ieu
Rwork0.163 ---
obs0.1663 41323 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.401→33.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 9 299 1810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151624
X-RAY DIFFRACTIONf_angle_d1.2762206
X-RAY DIFFRACTIONf_dihedral_angle_d12.799610
X-RAY DIFFRACTIONf_chiral_restr0.08236
X-RAY DIFFRACTIONf_plane_restr0.006290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.401-1.41750.37481160.34611230X-RAY DIFFRACTION98
1.4175-1.43480.3251460.33211271X-RAY DIFFRACTION100
1.4348-1.4530.31111290.30711264X-RAY DIFFRACTION100
1.453-1.47210.3251520.29561245X-RAY DIFFRACTION100
1.4721-1.49230.27651310.27351266X-RAY DIFFRACTION100
1.4923-1.51360.26431570.24641267X-RAY DIFFRACTION100
1.5136-1.53620.24461350.21761253X-RAY DIFFRACTION100
1.5362-1.56020.25291480.21281244X-RAY DIFFRACTION100
1.5602-1.58580.20251480.19841247X-RAY DIFFRACTION100
1.5858-1.61310.1971450.19041269X-RAY DIFFRACTION100
1.6131-1.64240.21471210.17951280X-RAY DIFFRACTION100
1.6424-1.6740.21831450.17861277X-RAY DIFFRACTION100
1.674-1.70820.21021410.16611258X-RAY DIFFRACTION100
1.7082-1.74530.19631410.16751276X-RAY DIFFRACTION100
1.7453-1.78590.20391390.16221270X-RAY DIFFRACTION100
1.7859-1.83060.19221320.15781269X-RAY DIFFRACTION100
1.8306-1.88010.17721190.1571296X-RAY DIFFRACTION100
1.8801-1.93540.211310.16211299X-RAY DIFFRACTION100
1.9354-1.99790.19361530.14671270X-RAY DIFFRACTION100
1.9979-2.06920.19741550.16411265X-RAY DIFFRACTION100
2.0692-2.15210.16951370.14521292X-RAY DIFFRACTION100
2.1521-2.250.2131290.15281299X-RAY DIFFRACTION100
2.25-2.36860.18481380.15031299X-RAY DIFFRACTION100
2.3686-2.5170.19721290.15341306X-RAY DIFFRACTION100
2.517-2.71120.21581670.15391288X-RAY DIFFRACTION100
2.7112-2.98390.20011350.16541313X-RAY DIFFRACTION100
2.9839-3.41540.18331520.14581335X-RAY DIFFRACTION100
3.4154-4.30160.16211400.13051356X-RAY DIFFRACTION100
4.3016-33.91680.15591620.14051446X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.2465 Å / Origin y: 2.9767 Å / Origin z: -49.8906 Å
111213212223313233
T0.0823 Å2-0.004 Å2-0.0021 Å2-0.0965 Å20.0048 Å2--0.0911 Å2
L0.7375 °20.2321 °2-0.2105 °2-0.7058 °2-0.0162 °2--0.7559 °2
S-0.0005 Å °0.0049 Å °-0.022 Å °0.0092 Å °0.0075 Å °-0.0117 Å °0.0457 Å °-0.0282 Å °-0.0004 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://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