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- PDB-4jto: Cysteine bound Cysteine Dioxygenase at pH 8.0 in the presence of ... -

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Basic information

Entry
Database: PDB / ID: 4jto
TitleCysteine bound Cysteine Dioxygenase at pH 8.0 in the presence of Cys and dithionite
ComponentsCysteine dioxygenase type 1
KeywordsOXIDOREDUCTASE / Cupin Fold / cysteine to cysteine sulfinic acid catalysis / Cytosol
Function / homology
Function and homology information


L-cysteine metabolic process / Degradation of cysteine and homocysteine / taurine biosynthetic process / cysteine dioxygenase / cysteine dioxygenase activity / response to azide / L-cysteine catabolic process / cysteine metabolic process / response to glucagon / nickel cation binding ...L-cysteine metabolic process / Degradation of cysteine and homocysteine / taurine biosynthetic process / cysteine dioxygenase / cysteine dioxygenase activity / response to azide / L-cysteine catabolic process / cysteine metabolic process / response to glucagon / nickel cation binding / response to cAMP / response to amino acid / lactation / response to glucocorticoid / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDriggers, C.M. / Karplus, P.A.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Cysteine Dioxygenase Structures from pH4 to 9: Consistent Cys-Persulfenate Formation at Intermediate pH and a Cys-Bound Enzyme at Higher pH.
Authors: Driggers, C.M. / Cooley, R.B. / Sankaran, B. / Hirschberger, L.L. / Stipanuk, M.H. / Karplus, P.A.
History
DepositionMar 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Sep 11, 2013Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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

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Assembly

Deposited unit
A: Cysteine dioxygenase type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2363
Polymers23,0591
Non-polymers1772
Water2,288127
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-5-

GLU

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Components

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


Mass: 23058.889 Da / Num. of mol.: 1
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-FE2 / FE (II) ION


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


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M tri-sodium citrate pH=5.6, 24% PEG 4000, 0.15M ammonium acetate. 1:1 drop ratio with microseeding, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 1, 2013 / Details: Osmic
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→29 Å / Num. all: 13313 / Num. obs: 13313 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28.034 Å / SU ML: 0.22 / σ(F): 1.33 / Phase error: 24.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 1251 9.76 %Same test set 4IEU
Rwork0.1757 ---
obs0.1814 12817 86.25 %-
all-13313 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→28.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 8 127 1639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141561
X-RAY DIFFRACTIONf_angle_d1.372117
X-RAY DIFFRACTIONf_dihedral_angle_d14.804568
X-RAY DIFFRACTIONf_chiral_restr0.083227
X-RAY DIFFRACTIONf_plane_restr0.006274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9874-2.0670.30591500.21491222X-RAY DIFFRACTION86
2.067-2.1610.26471300.2091223X-RAY DIFFRACTION84
2.161-2.27490.4662720.3388753X-RAY DIFFRACTION51
2.2749-2.41730.29611370.20681456X-RAY DIFFRACTION98
2.4173-2.60390.27561690.18531454X-RAY DIFFRACTION100
2.6039-2.86570.23661330.18531240X-RAY DIFFRACTION84
2.8657-3.27980.26781680.1861480X-RAY DIFFRACTION100
3.2798-4.13010.20141220.16781158X-RAY DIFFRACTION75
4.1301-28.03720.17761700.13771580X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -17.2034 Å / Origin y: 3.3807 Å / Origin z: -49.6877 Å
111213212223313233
T0.1079 Å20.001 Å2-0.0037 Å2-0.1537 Å2-0.0022 Å2--0.1251 Å2
L1.4532 °20.426 °2-0.3003 °2-1.2622 °20.0089 °2--0.8892 °2
S-0.0095 Å °0.0215 Å °-0.0262 Å °-0.032 Å °-0.0148 Å °-0.0062 Å °0.0501 Å °-0.0276 Å °0.0205 Å °
Refinement TLS groupSelection details: all

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