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- PDB-6bpr: Crystal structure of cysteine, nitric oxide-bound ferrous form of... -

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Basic information

Entry
Database: PDB / ID: 6bpr
TitleCrystal structure of cysteine, nitric oxide-bound ferrous form of the uncrosslinked F2-Tyr157 human cysteine dioxygenase
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 / : / NITRIC OXIDE / Cysteine dioxygenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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: Biochemistry / Year: 2019
Title: Probing the Cys-Tyr Cofactor Biogenesis in Cysteine Dioxygenase by the Genetic Incorporation of Fluorotyrosine.
Authors: Li, J. / Koto, T. / Davis, I. / Liu, A.
History
DepositionNov 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 2019Group: 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 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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.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 1.5Nov 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)24,12214
Polymers22,9821
Non-polymers1,14013
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-52 kcal/mol
Surface area9700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.306, 131.306, 34.175
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: 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

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Non-polymers , 6 types, 204 molecules

#2: Chemical ChemComp-FE / FE (III) 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: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 3.7 Å3/Da / Density % sol: 66.76 %
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: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 13, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 24681 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 26.43 Å2 / Rmerge(I) obs: 0.143 / Χ2: 1.067 / Net I/σ(I): 5 / Num. measured all: 273552
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.96-1.99110.99912240.9221100
1.99-2.0311.10.86812230.9671100
2.03-2.0711.10.8411850.9681100
2.07-2.1111.20.76312271.0321100
2.11-2.1611.10.67312391.0311100
2.16-2.2111.20.62312061.031100
2.21-2.2611.20.51412341.0511100
2.26-2.3211.20.44712071.0921100
2.32-2.3911.20.4212421.0821100
2.39-2.4711.20.37812261.0961100
2.47-2.5611.20.3312161.1171100
2.56-2.6611.20.26412361.1761100
2.66-2.7811.20.22112201.1891100
2.78-2.9311.20.19612331.1881100
2.93-3.1111.20.14612421.2011100
3.11-3.3511.10.10412371.1711100
3.35-3.6911.10.08212431.1341100
3.69-4.2211.10.06612591.0371100
4.22-5.3210.90.05412560.8961100
5.32-5010.20.05813260.941199.7

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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: 1.96→32.827 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.188 2004 8.13 %
Rwork0.1605 22655 -
obs0.1628 24659 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.16 Å2 / Biso mean: 31.1334 Å2 / Biso min: 13.9 Å2
Refinement stepCycle: final / Resolution: 1.96→32.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 67 191 1770
Biso mean--49.11 40.81 -
Num. residues----186
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9598-2.00880.26251410.212916021743
2.0088-2.06310.23681390.211615911730
2.0631-2.12380.24041410.200316011742
2.1238-2.19240.24861390.194115851724
2.1924-2.27070.19211450.19416271772
2.2707-2.36160.20541370.1815741711
2.3616-2.4690.23591410.183116421783
2.469-2.59920.22091470.16916011748
2.5992-2.76190.18861390.168716171756
2.7619-2.97510.21561390.168816081747
2.9751-3.27420.16671480.156516191767
3.2742-3.74740.1611440.134216391783
3.7474-4.71910.17471440.121316431787
4.7191-32.83110.15391600.162717061866

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