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- PDB-6cdh: Crystal structure of ferrous form of the Cl-Tyr157 human cysteine... -

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Basic information

Entry
Database: PDB / ID: 6cdh
TitleCrystal structure of ferrous form of the Cl-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: 1.821 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
DepositionFeb 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
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

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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)23,5087
Polymers22,9801
Non-polymers5286
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, MONOMER
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-49 kcal/mol
Surface area9710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.426, 131.426, 34.241
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: 22980.201 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
#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.: 162 / 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: 66.8 %
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: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 30665 / % possible obs: 99.8 % / Redundancy: 6 % / Biso Wilson estimate: 28.98 Å2 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.071 / Rrim(I) all: 0.179 / Χ2: 1.094 / Net I/σ(I): 6.4 / Num. measured all: 185068
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.82-1.854.90.45215070.940.2240.5070.53499.8
1.85-1.895.30.40815250.9430.1940.4530.552100
1.89-1.925.70.36915170.9490.170.4070.596100
1.92-1.965.80.33615150.9590.1550.3710.6199.9
1.96-25.90.29415160.9570.1340.3240.71499.9
2-2.055.90.27115220.9580.1240.2990.717100
2.05-2.15.50.25715040.9560.1210.2850.80399.6
2.1-2.166.30.23315430.9660.1030.2550.79100
2.16-2.226.30.22215250.9620.0970.2420.812100
2.22-2.296.30.19415240.9730.0840.2120.89499.9
2.29-2.376.20.19315170.9690.0850.2110.946100
2.37-2.476.20.18915420.9640.0830.2071.04399.9
2.47-2.585.70.1815000.960.0820.1991.15899.4
2.58-2.726.50.17415250.970.0740.1891.18399.9
2.72-2.896.40.16815510.9710.0720.1831.32699.9
2.89-3.116.40.16615580.980.0710.181.527100
3.11-3.436.10.15915330.9730.070.1741.70899.5
3.43-3.926.70.16115460.9720.0670.1751.84999.9
3.92-4.946.20.15715720.9740.0680.1711.899.6
4.94-506.40.1516230.9670.0660.1651.71899.1

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Processing

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

2ic1


Resolution: 1.821→43.019 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1819 1997 6.52 %
Rwork0.1648 28628 -
obs0.1659 30625 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.99 Å2 / Biso mean: 36.26 Å2 / Biso min: 20.51 Å2
Refinement stepCycle: final / Resolution: 1.821→43.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1511 0 28 162 1701
Biso mean--56.54 46.63 -
Num. residues----186
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 (%)
1.8214-1.86690.25031380.20851943208196
1.8669-1.91740.20841440.190220562200100
1.9174-1.97380.19511370.178619952132100
1.9738-2.03760.17991460.172820352181100
2.0376-2.11040.23421430.17252030217399
2.1104-2.19490.2021410.174520262167100
2.1949-2.29480.19641430.173420542197100
2.2948-2.41570.2061420.177520412183100
2.4157-2.56710.19371430.1820382181100
2.5671-2.76520.21271460.173920472193100
2.7652-3.04350.17041390.183320562195100
3.0435-3.48370.17541430.159820782221100
3.4837-4.38840.13071470.13920842231100
4.3884-43.03120.19741450.16132145229099

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