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- PDB-6bgf: Crystal structure of cysteine-bound ferrous form of the crosslink... -

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Basic information

Entry
Database: PDB / ID: 6bgf
TitleCrystal structure of cysteine-bound ferrous form of the crosslinked human cysteine dioxygenase
ComponentsCysteine dioxygenase type 1
KeywordsOXIDOREDUCTASE / Cysteine / Cys-Tyr cofactor / iron
Function / homology
Function and homology information


sulfur amino acid biosynthetic 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 ...sulfur amino acid biosynthetic 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 amino acid / response to glucocorticoid / response to cAMP / lactation / ferrous iron binding / response to ethanol / inflammatory response / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.251 Å
AuthorsLiu, A. / Li, J. / Shin, I.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1623856 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM107529 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108988 United States
CitationJournal: Nat.Chem.Biol. / Year: 2018
Title: Cleavage of a carbon-fluorine bond by an engineered cysteine dioxygenase.
Authors: Li, J. / Griffith, W.P. / Davis, I. / Shin, I. / Wang, J. / Li, F. / Wang, Y. / Wherritt, D.J. / Liu, A.
History
DepositionOct 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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

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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)23,87111
Polymers22,9461
Non-polymers92610
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, MONOMER
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-36 kcal/mol
Surface area9930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.295, 131.295, 34.218
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 22945.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDO1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16878, cysteine dioxygenase

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Non-polymers , 5 types, 114 molecules

#2: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.71 Å3/Da / Density % sol: 66.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES, 2 M ammonium sulfate, 2% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 16168 / % possible obs: 98.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 37.89 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.037 / Rrim(I) all: 0.091 / Χ2: 1.052 / Net I/σ(I): 9.1 / Num. measured all: 87856
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.313.70.41911450.6420.220.4771.20792
2.31-2.384.20.37211770.9010.1930.4210.60695.9
2.38-2.4650.37412420.8710.1820.4170.66299
2.46-2.544.80.33112290.9180.1630.3710.66799.9
2.54-2.655.80.26312630.9610.1190.2890.721100
2.65-2.7760.22112370.9690.0970.2420.841100
2.77-2.9160.17312560.9840.0760.190.795100
2.91-3.0960.13312390.9890.0580.1450.9799.2
3.09-3.335.40.09612430.9910.0440.1061.19199.3
3.33-3.676.10.08112580.9950.0350.0881.44999.8
3.67-4.26.10.0612810.9970.0260.0651.428100
4.2-5.295.60.04912590.9980.0220.0541.46799.1
5.29-505.80.04713390.9980.0220.0521.39799.5

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Processing

Software
NameVersionClassification
PHENIXrefinement
DENZOdata collection
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2IC1

2ic1


Resolution: 2.251→37.902 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2193 1594 9.87 %
Rwork0.1648 14555 -
obs0.1699 16149 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.65 Å2 / Biso mean: 42.8225 Å2 / Biso min: 24.89 Å2
Refinement stepCycle: final / Resolution: 2.251→37.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1523 0 46 104 1673
Biso mean--61.7 46.47 -
Num. residues----189
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.251-2.32370.30651250.24181176130189
2.3237-2.40670.26591400.2291283142397
2.4067-2.50310.28181510.223613181469100
2.5031-2.6170.25151500.204113431493100
2.617-2.75490.23771480.177912981446100
2.7549-2.92740.22191460.181513441490100
2.9274-3.15340.24391460.17981345149199
3.1534-3.47050.21941500.15111322147299
3.4705-3.97220.21081460.144213441490100
3.9722-5.00280.17491400.12591366150699
5.0028-37.9070.20651520.167814161568100

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