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- PDB-3f0i: Arsenate reductase from Vibrio cholerae. -

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Basic information

Entry
Database: PDB / ID: 3f0i
TitleArsenate reductase from Vibrio cholerae.
ComponentsArsenate reductase
KeywordsOXIDOREDUCTASE / structural genomics / IDP01300 / Arsenate reductase / Vibrio cholerae. / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


arsenate reductase (glutathione/glutaredoxin) / arsenate reductase (glutaredoxin) activity / response to arsenic-containing substance / cytosol
Similarity search - Function
Arsenate reductase / Arsenate reductase-like / ArsC family / ArsC family profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / Arsenate reductase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å
AuthorsOsipiuk, J. / Gu, M. / Stam, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: X-ray crystal structure of Arsenate reductase from Vibrio cholerae.
Authors: Osipiuk, J. / Gu, M. / Stam, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionOct 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arsenate reductase
B: Arsenate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5275
Polymers27,3002
Non-polymers2273
Water5,423301
1
A: Arsenate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7753
Polymers13,6501
Non-polymers1252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arsenate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7522
Polymers13,6501
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.704, 118.704, 110.013
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-503-

NA

21A-153-

HOH

31A-158-

HOH

Detailsputative biological unit is a monomer

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Components

#1: Protein Arsenate reductase


Mass: 13650.100 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O1 biovar eltor str. N16961 / Gene: VC2165, VC_2165 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KQ39
#2: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 4.1 Å3/Da / Density % sol: 69.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.4 M sodium malonate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792
DetectorType: SBC-3 / Detector: CCD / Date: Oct 2, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.88→31.7 Å / Num. all: 37716 / Num. obs: 37716 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.09 / Χ2: 1.777 / Net I/σ(I): 39.832
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 2.04 / Num. unique all: 1841 / Χ2: 0.745 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0054refinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.88→31.7 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0 / SU B: 4.33 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.093 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.189 1863 5 %RANDOM
Rwork0.166 ---
all0.167 37124 --
obs0.167 37124 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.13 Å2 / Biso mean: 23.387 Å2 / Biso min: 12.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20.3 Å20 Å2
2--0.61 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.88→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1874 0 15 301 2190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221996
X-RAY DIFFRACTIONr_bond_other_d0.0010.021391
X-RAY DIFFRACTIONr_angle_refined_deg1.5342.0062710
X-RAY DIFFRACTIONr_angle_other_deg0.91633440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3475258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31625.46497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99315390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9431514
X-RAY DIFFRACTIONr_chiral_restr0.0950.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212226
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02344
X-RAY DIFFRACTIONr_mcbond_it0.911.51228
X-RAY DIFFRACTIONr_mcbond_other0.2541.5481
X-RAY DIFFRACTIONr_mcangle_it1.64821997
X-RAY DIFFRACTIONr_scbond_it2.7113768
X-RAY DIFFRACTIONr_scangle_it4.5134.5702
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 153 -
Rwork0.239 2562 -
all-2715 -
obs-2712 99.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3910.5661-0.43090.4821-0.10310.2351-0.0037-0.1751-0.2120.0371-0.071-0.16250.0384-0.00440.07460.06550.00060.01380.09210.03790.072376.809927.80880.3886
20.7530.7123-0.11332.66220.34710.5229-0.0138-0.18040.0841-0.141-0.08940.0883-0.0431-0.06120.10320.01540.0108-0.00540.1067-0.03820.044573.034254.969-7.2604
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 116
2X-RAY DIFFRACTION2B-1 - 116

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