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- PDB-6bgm: Crystal structure of ferrous form of the crosslinked human cystei... -

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Basic information

Entry
Database: PDB / ID: 6bgm
TitleCrystal structure of 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 cAMP / response to amino acid / lactation / response to glucocorticoid / 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 dioxygenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.206 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 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 13, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jul 4, 2018Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.4Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.5Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.6Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Oct 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

Downloads & links

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Assembly

Deposited unit
A: Cysteine dioxygenase type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4747
Polymers22,9461
Non-polymers5286
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, MONOMER
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-46 kcal/mol
Surface area10090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.757, 131.757, 34.262
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#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
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 3.74 Å3/Da / Density % sol: 67.12 %
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: Jan 14, 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: 2.2→50 Å / Num. obs: 17488 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 40.71 Å2 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.069 / Rrim(I) all: 0.198 / Χ2: 1.071 / Net I/σ(I): 5.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.266.60.83913450.8230.3490.9120.82100
2.26-2.337.21.04413090.8230.4131.1260.67399.8
2.33-2.46.70.78113280.850.3230.8480.706100
2.4-2.498.50.72713320.8720.2650.7760.799.9
2.49-2.598.80.55513310.9420.1990.590.723100
2.59-2.78.80.43613440.9530.1560.4630.835100
2.7-2.858.70.34813470.9710.1260.3710.854100
2.85-3.038.80.28913130.9710.1040.3081.006100
3.03-3.268.50.22513440.9790.0820.241.305100
3.26-3.597.50.18913530.9790.0730.2031.64199.9
3.59-4.118.80.16613580.9860.0610.1771.694100
4.11-5.178.30.13213620.990.050.1411.499100
5.17-508.10.11414220.9920.0430.1221.30798.9

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Processing

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

2ic1


Resolution: 2.206→32.939 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.96
RfactorNum. reflection% reflection
Rfree0.216 1753 10.04 %
Rwork0.1793 --
obs0.183 17462 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.34 Å2 / Biso mean: 46.7922 Å2 / Biso min: 26.21 Å2
Refinement stepCycle: final / Resolution: 2.206→32.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 28 72 1614
Biso mean--67.71 51.63 -
Num. residues----187
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2055-2.26520.44171310.38421137126894
2.2652-2.33180.32961300.30111751305100
2.3318-2.4070.31561340.259912111345100
2.407-2.4930.28471310.231412001331100
2.493-2.59280.25061320.211711971329100
2.5928-2.71080.2521350.193312041339100
2.7108-2.85360.28391370.19312231360100
2.8536-3.03230.24471370.203711931330100
3.0323-3.26620.20971360.17811981334100
3.2662-3.59460.19281340.152812281362100
3.5946-4.11390.16511390.14112201359100
4.1139-5.17980.15341350.137812401375100
5.1798-32.94290.20721420.17591283142599

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