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- PDB-1jl3: Crystal Structure of B. subtilis ArsC -

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Basic information

Entry
Database: PDB / ID: 1jl3
TitleCrystal Structure of B. subtilis ArsC
ComponentsARSENATE REDUCTASE
KeywordsOXIDOREDUCTASE / alpha-beta fold / PTP-loop / arsenate reductase
Function / homology
Function and homology information


arsenate reductase (thioredoxin) / arsenate reductase (thioredoxin) activity / response to arsenic-containing substance / protein tyrosine phosphatase activity / cytoplasm
Similarity search - Function
Arsenate reductase ArsC / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsSu, X.-D. / Bennett, M.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Bacillus subtilis arsenate reductase is structurally and functionally similar to low molecular weight protein tyrosine phosphatases.
Authors: Bennett, M.S. / Guan, Z. / Laurberg, M. / Su, X.D.
History
DepositionJul 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: ARSENATE REDUCTASE
B: ARSENATE REDUCTASE
C: ARSENATE REDUCTASE
D: ARSENATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8428
Polymers62,4584
Non-polymers3844
Water4,684260
1
A: ARSENATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7112
Polymers15,6141
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ARSENATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7112
Polymers15,6141
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ARSENATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7112
Polymers15,6141
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ARSENATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7112
Polymers15,6141
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.940, 94.310, 118.700
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
ARSENATE REDUCTASE


Mass: 15614.480 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: arsC / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P45947
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 4000, ammonium sulfate, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal grow
*PLUS
PH range low: 4.6 / PH range high: 4.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium acetate1reservoir
20.2 Mammonium sulfate1reservoir
330-35 %polyethyleneglycol methyl1reservoir
45 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.9999, 0.9700, 0.9500
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 8, 2001
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.99991
20.971
30.951
ReflectionResolution: 1.6→27 Å / Num. all: 76313 / Num. obs: 74177 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 4.2 / Net I/σ(I): 19
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.92 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 4.6 / Num. unique all: 12202 / Rsym value: 29.3 / % possible all: 97.4
Reflection
*PLUS
Lowest resolution: 26.8 Å / % possible obs: 97.3 % / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.7 Å / % possible obs: 97.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.7

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.6→26.75 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2063791.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Chain A and B have complete and correct suqeunces from 3 to 139, however, residues from 39 to 41 are slightly disordered. Chain C only contains 121 residues, the missing ones are disordered, ...Details: Chain A and B have complete and correct suqeunces from 3 to 139, however, residues from 39 to 41 are slightly disordered. Chain C only contains 121 residues, the missing ones are disordered, not visible from the maps. Chain D only contains 122 residues, the missing ones are disordered, not visible from the maps. The C-term Lys residues have weak densities, thus some of these Lys contain missing atoms.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3796 5.1 %RANDOM
Rwork0.226 ---
all0.226 74177 --
obs0.226 74177 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.6342 Å2 / ksol: 0.399454 e/Å3
Displacement parametersBiso mean: 18.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20 Å2
2--1.26 Å20 Å2
3---0.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.6→26.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4090 0 20 260 4370
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 622 5.1 %
Rwork0.239 11609 -
obs--97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER.PARAM
Refinement
*PLUS
Lowest resolution: 26.8 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.64

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