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- PDB-3mwh: The 1.4 Ang crystal structure of the ArsD arsenic metallochaperon... -

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Basic information

Entry
Database: PDB / ID: 3mwh
TitleThe 1.4 Ang crystal structure of the ArsD arsenic metallochaperone provides insights into its interactions with the ArsA ATPase
ComponentsArsenical resistance operon trans-acting repressor arsD
KeywordsCHAPERONE / ALPHA+BETA / ARSENICAL RESISTANCE / 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 / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsYe, J. / Ajees, A.A. / Yang, 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
DepositionMay 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Database references / Category: citation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,1343
Polymers24,0422
Non-polymers921
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-5 kcal/mol
Surface area11090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.676, 74.223, 40.830
Angle α, β, γ (deg.)90.00, 97.77, 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: 12020.948 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: arsD, R773 / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P46003
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 25% PEG 6000, 0.1M Calcium acetate, 0.1M HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 13, 2007 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→40.46 Å / Num. obs: 13712 / % possible obs: 97.8 % / Redundancy: 3.12 % / Rsym value: 0.091
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.05 % / Rmerge(I) obs: 0.348 / Num. unique all: 13712 / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KGK

3kgk


Resolution: 2.05→40.46 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.892 / SU B: 13.46 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32419 686 5 %RANDOM
Rwork0.27098 ---
obs0.27351 13712 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å21.52 Å2
2---2.05 Å20 Å2
3---3.34 Å2
Refinement stepCycle: LAST / Resolution: 2.05→40.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1534 0 6 113 1653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221568
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9921.9792115
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3745192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.86525.07269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.26715278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.935158
X-RAY DIFFRACTIONr_chiral_restr0.1410.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211164
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_it1.1291.5973
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.96621558
X-RAY DIFFRACTIONr_scbond_it3.1483595
X-RAY DIFFRACTIONr_scangle_it4.74.5557
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 53 -
Rwork0.297 945 -
obs--98.52 %
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)
16.1826-5.48777.34678.8639-6.979210.3233-0.17020.08120.01250.29760.02230.4128-0.13040.11890.14790.1639-0.02010.03020.16970.0280.09468.9193-1.223117.5849
22.3382-0.7364-0.57073.13010.5531.3931-0.0930.0289-0.17280.03530.00040.23840.2257-0.01240.09250.153-0.0067-0.02610.10760.00190.039210.7563-1.40413.0067
37.9864-6.1839-2.07958.8351-0.71871.55210.01530.33620.29490.404-0.2904-0.1677-0.0301-0.12180.27510.16910.02880.02780.189-0.06350.308820.980919.463711.0183
41.4043-0.04390.14421.973-0.97282.98570.03230.03920.1984-0.11490.024-0.1022-0.0130.1019-0.05640.0924-0.0065-0.00620.0949-0.00660.043719.726817.20547.3213
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 9
2X-RAY DIFFRACTION2A20 - 109
3X-RAY DIFFRACTION3B1 - 10
4X-RAY DIFFRACTION4B23 - 108

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