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- PDB-6xck: Crystal structure of C-As lyase with mutation K105E -

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Basic information

Entry
Database: PDB / ID: 6xck
TitleCrystal structure of C-As lyase with mutation K105E
ComponentsGlyoxalase/bleomycin resistance protein/dioxygenase
KeywordsOXIDOREDUCTASE / C-As lyase
Function / homology: / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / dioxygenase activity / metal ion binding / Glyoxalase/bleomycin resistance protein/dioxygenase
Function and homology information
Biological speciesThermomonospora curvata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsVenkadesh, S. / Yoshinaga, M. / Kandavelu, P. / Sankaran, B. / Rosen, B.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37 GM055425 United States
CitationJournal: J.Inorg.Biochem. / Year: 2022
Title: The ArsI C-As lyase: Elucidating the catalytic mechanism of degradation of organoarsenicals.
Authors: Nadar, V.S. / Kandavelu, P. / Sankaran, B. / Rosen, B.P. / Yoshinaga, M.
History
DepositionJun 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyoxalase/bleomycin resistance protein/dioxygenase
B: Glyoxalase/bleomycin resistance protein/dioxygenase


Theoretical massNumber of molelcules
Total (without water)26,9062
Polymers26,9062
Non-polymers00
Water3,603200
1
A: Glyoxalase/bleomycin resistance protein/dioxygenase


Theoretical massNumber of molelcules
Total (without water)13,4531
Polymers13,4531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glyoxalase/bleomycin resistance protein/dioxygenase


Theoretical massNumber of molelcules
Total (without water)13,4531
Polymers13,4531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-28 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.250, 43.195, 119.431
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glyoxalase/bleomycin resistance protein/dioxygenase


Mass: 13453.017 Da / Num. of mol.: 2 / Mutation: K105E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9) (bacteria)
Strain: ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9
Gene: Tcur_4156 / Production host: Escherichia coli (E. coli) / References: UniProt: D1A230
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.04 Å3/Da / Density % sol: 39.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Calcium acetate, 0.1 M Tris-HCl, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 31, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 28571 / % possible obs: 99.5 % / Redundancy: 24 % / CC1/2: 0.9911 / Rpim(I) all: 0.017 / Rrim(I) all: 0.065 / Net I/σ(I): 36.3
Reflection shellResolution: 1.62→1.68 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 5.4 / Num. unique obs: 2845 / CC1/2: 0.972 / Rpim(I) all: 0.147 / Rrim(I) all: 0.556 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V0F

5v0f


Resolution: 1.62→30.204 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2538 1412 5.08 %RANDOM
Rwork0.2145 ---
obs0.2164 27802 96.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.62→30.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1619 0 0 200 1819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071767
X-RAY DIFFRACTIONf_angle_d1.2272421
X-RAY DIFFRACTIONf_dihedral_angle_d14.793637
X-RAY DIFFRACTIONf_chiral_restr0.083275
X-RAY DIFFRACTIONf_plane_restr0.007322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.6760.26171130.23092149X-RAY DIFFRACTION80
1.676-1.74310.31581580.24242456X-RAY DIFFRACTION93
1.7431-1.82250.31371440.24332660X-RAY DIFFRACTION99
1.8225-1.91850.30451580.23652687X-RAY DIFFRACTION100
1.9185-2.03870.25681360.22122695X-RAY DIFFRACTION100
2.0387-2.19610.2431380.22282694X-RAY DIFFRACTION100
2.1961-2.4170.25281430.22052732X-RAY DIFFRACTION100
2.417-2.76650.25821360.2222741X-RAY DIFFRACTION100
2.7665-3.48470.23011360.20322770X-RAY DIFFRACTION100
3.4847-30.2040.2281500.19212806X-RAY DIFFRACTION96

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