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- PDB-3kgk: Crystal structure of ArsD -

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Basic information

Entry
Database: PDB / ID: 3kgk
TitleCrystal structure of ArsD
ComponentsArsenical resistance operon trans-acting repressor arsD
KeywordsCHAPERONE / alpha+beta / Arsenical resistance / DNA-binding / Repressor / Transcription / Transcription regulation
Function / homology
Function and homology information


response to arsenic-containing substance / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Arsenical-resistance operon trans-acting repressor ArsD / Arsenical resistance operon protein ArsD / Glutaredoxin / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Arsenical resistance operon trans-acting repressor ArsD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsYe, J. / Rosen, B.P.
CitationJournal: Biochemistry / Year: 2010
Title: The 1.4 A crystal structure of the ArsD arsenic metallochaperone provides insights into its interaction with the ArsA ATPase.
Authors: Ye, J. / Ajees, A.A. / Yang, J. / Rosen, B.P.
History
DepositionOct 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arsenical resistance operon trans-acting repressor arsD
B: Arsenical resistance operon trans-acting repressor arsD


Theoretical massNumber of molelcules
Total (without water)23,8822
Polymers23,8822
Non-polymers00
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.841, 73.774, 41.248
Angle α, β, γ (deg.)90.00, 97.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Arsenical resistance operon trans-acting repressor arsD


Mass: 11940.753 Da / Num. of mol.: 2 / Fragment: UNP residues 1-109 / Mutation: C12A, C13A, C39S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: arsD / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46003
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 25% PEG 6000, 0.1 M calcium acetate, 0.1 M HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 13, 2007 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→40.9 Å / Num. all: 44159 / Num. obs: 43232 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rsym value: 0.051 / Net I/σ(I): 16
Reflection shellResolution: 1.4→1.52 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 6273 / Rsym value: 0.438 / % possible all: 97.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.5.0046refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.4→35.78 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.167 / SU ML: 0.039 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21912 2171 5 %RANDOM
Rwork0.19212 ---
obs0.19348 41036 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.299 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20.18 Å2
2---0.18 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.4→35.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1492 0 0 268 1760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221521
X-RAY DIFFRACTIONr_angle_refined_deg1.1571.9762052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0995186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.80824.92567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24315272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.17158
X-RAY DIFFRACTIONr_chiral_restr0.080.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211132
X-RAY DIFFRACTIONr_mcbond_it0.6511.5944
X-RAY DIFFRACTIONr_mcangle_it1.24421511
X-RAY DIFFRACTIONr_scbond_it1.9093577
X-RAY DIFFRACTIONr_scangle_it3.1814.5541
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 162 -
Rwork0.277 3026 -
obs--97.25 %
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)
16.4234-3.97275.21455.7572-4.67966.6275-0.01790.0085-0.00910.1221-0.07820.19380.1430.00060.09610.0408-0.00360.04690.03040.02640.09497.921-0.77316.816
21.621-0.4088-0.50692.06730.2861.0717-0.076-0.0552-0.05440.03270.06630.15460.1731-0.00560.00960.03590.00360.01390.01450.01460.055110.117-0.39213.619
310.0586-7.1447-1.41637.13040.81442.70.15780.09030.2031-0.0521-0.23020.0202-0.16780.01910.07250.0137-0.00560.00940.0158-0.01330.101121.04318.91510.797
40.7310.02420.16571.8643-0.83391.69770.01430.00330.1382-0.06120.0174-0.0616-0.01810.0441-0.03170.0144-0.00120.02870.01650.00010.082719.66617.1157.142
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 10
2X-RAY DIFFRACTION2A24 - 105
3X-RAY DIFFRACTION3B1 - 10
4X-RAY DIFFRACTION4B23 - 109

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