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- PDB-6bpu: Crystal structure of ferrous form of the F2-Tyr157 human cysteine... -

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Basic information

Entry
Database: PDB / ID: 6bpu
TitleCrystal structure of ferrous form of the F2-Tyr157 human cysteine dioxygenase with both uncrosslinked and crosslinked cofactor
ComponentsCysteine dioxygenase type 1
KeywordsOXIDOREDUCTASE / Cysteine / Cys-Tyr cofactor / iron / unnatural amino acid
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: 1.8 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
DepositionNov 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.2Aug 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 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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 / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.6Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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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)23,6949
Polymers22,9821
Non-polymers7128
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, MONOMER
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-48 kcal/mol
Surface area9870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.385, 131.385, 34.246
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: 22981.736 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 66.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / 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: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 32023 / % possible obs: 99.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 28.68 Å2 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.076 / Rrim(I) all: 0.222 / Χ2: 1.029 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8440.67820190.8560.3360.7610.45696.8
1.84-1.894.90.55421070.9030.2540.6120.48799.5
1.89-1.945.60.54421300.9260.2380.5950.51499.9
1.94-26.10.4221040.9620.1750.4560.568100
2-2.066.20.40721270.9490.1690.4420.63100
2.06-2.137.10.36721310.9640.1440.3950.639100
2.13-2.227.70.36621200.9440.140.3920.678100
2.22-2.327.80.31921350.9630.120.3410.747100
2.32-2.4480.31121430.9650.1160.3320.798100
2.44-2.680.28421180.9650.1060.3030.89499.9
2.6-2.88.80.25521430.9630.0910.2711.056100
2.8-3.088.70.22821520.9690.0820.2431.295100
3.08-3.528.50.20821470.9710.0750.2211.698100
3.52-4.448.90.19321840.9750.0680.2051.905100
4.44-508.40.1722630.980.0620.1811.68999.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2IC1

2ic1


Resolution: 1.8→37.928 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.71
RfactorNum. reflection% reflection
Rfree0.1892 2006 6.28 %
Rwork0.1682 --
obs0.1695 31938 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.44 Å2 / Biso mean: 35.5249 Å2 / Biso min: 18.64 Å2
Refinement stepCycle: final / Resolution: 1.8→37.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 40 156 1716
Biso mean--56.28 45.15 -
Num. residues----187
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7938-1.83870.32871300.29291960209094
1.8387-1.88840.24461450.2382138228399
1.8884-1.9440.21671420.20642096223899
1.944-2.00670.21371440.18842136228099
2.0067-2.07840.2221400.186821062246100
2.0784-2.16160.23911420.180821442286100
2.1616-2.260.19621440.175921452289100
2.26-2.37910.24431400.179121282268100
2.3791-2.52820.19581450.180921512296100
2.5282-2.72330.18481430.177421302273100
2.7233-2.99730.231440.183921712315100
2.9973-3.43080.18431470.162621822329100
3.4308-4.32140.14751480.136921792327100
4.3214-37.9360.16891520.156122662418100

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