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- PDB-5c4p: Crystal structure of ArsI C-As lyase solved by Ni-SAD phasing -

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Basic information

Entry
Database: PDB / ID: 5c4p
TitleCrystal structure of ArsI C-As lyase solved by Ni-SAD phasing
ComponentsGlyoxalase/bleomycin resistance protein/dioxygenase
KeywordsOXIDOREDUCTASE / C-As lyase / Ni-SAD / Arsenic
Function / homology
Function and homology information


Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / dioxygenase activity / response to cadmium ion / metal ion binding
Similarity search - Function
: / : / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Trivalent organoarsenical cleaving enzyme
Similarity search - Component
Biological speciesThermomonospora curvata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å
AuthorsVenkadesh, S. / Yoshinaga, M. / Kandavelu, P. / Rosen, B.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37 GM55425 United States
CitationJournal: To Be Published
Title: Crystal structure of ArsI C-As lyase from Thermomonospora curvata
Authors: Venkadesh, S. / Yoshinaga, M. / Kandavelu, P. / Rosen, B.P.
History
DepositionJun 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5122
Polymers13,4531
Non-polymers591
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-10 kcal/mol
Surface area6520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.843, 42.843, 118.176
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-334-

HOH

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Components

#1: Protein Glyoxalase/bleomycin resistance protein/dioxygenase


Mass: 13453.083 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / NCIMB 10081) (bacteria)
Strain: ATCC 19995 / DSM 43183 / JCM 3096 / NCIMB 10081 / Gene: Tcur_4156 / Production host: Escherichia coli (E. coli) / References: UniProt: D1A230
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, 0.2 M Calcium acetate, 0.1 M Tris-HCl / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.47899 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 31, 2013
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.47899 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 8156 / % possible obs: 97.3 % / Redundancy: 20.6 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 27.5
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 5.2 / % possible all: 78.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.97→40.28 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.205 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26454 377 4.6 %RANDOM
Rwork0.20531 ---
obs0.20779 7779 97.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.474 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.97→40.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms809 0 1 49 859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.019856
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0681.9711170
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9635114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51424.11834
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.88915124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.028155
X-RAY DIFFRACTIONr_chiral_restr0.1690.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021662
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 28 -
Rwork0.318 452 -
obs--78.3 %

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