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- PDB-3ktb: Crystal Structure of Arsenical Resistance Operon Trans-acting Rep... -

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Basic information

Entry
Database: PDB / ID: 3ktb
TitleCrystal Structure of Arsenical Resistance Operon Trans-acting Repressor from Bacteroides vulgatus ATCC 8482
ComponentsArsenical resistance operon trans-acting repressor
Keywordstranscription regulator / alpha-beta-alpha sandwich / helix-turn-helix / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


response to arsenic-containing substance / negative regulation of DNA-templated transcription / DNA binding / metal ion binding
Similarity search - Function
Arsenical-resistance operon trans-acting repressor ArsD / Arsenical resistance operon protein ArsD / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Arsenical resistance operon trans-acting repressor
Similarity search - Component
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsKim, Y. / Tesar, C. / Feldmann, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Arsenical Resistance Operon Trans-acting Repressor from Bacteroides vulgatus ATCC 8482
Authors: Kim, Y. / Tesar, C. / Feldmann, B. / Joachimiak, A.
History
DepositionNov 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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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
B: Arsenical resistance operon trans-acting repressor
C: Arsenical resistance operon trans-acting repressor
D: Arsenical resistance operon trans-acting repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,10110
Polymers47,6644
Non-polymers4366
Water8,773487
1
A: Arsenical resistance operon trans-acting repressor
B: Arsenical resistance operon trans-acting repressor
C: Arsenical resistance operon trans-acting repressor
D: Arsenical resistance operon trans-acting repressor
hetero molecules

A: Arsenical resistance operon trans-acting repressor
B: Arsenical resistance operon trans-acting repressor
C: Arsenical resistance operon trans-acting repressor
D: Arsenical resistance operon trans-acting repressor
hetero molecules

A: Arsenical resistance operon trans-acting repressor
B: Arsenical resistance operon trans-acting repressor
C: Arsenical resistance operon trans-acting repressor
D: Arsenical resistance operon trans-acting repressor
hetero molecules

A: Arsenical resistance operon trans-acting repressor
B: Arsenical resistance operon trans-acting repressor
C: Arsenical resistance operon trans-acting repressor
D: Arsenical resistance operon trans-acting repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,40340
Polymers190,65716
Non-polymers1,74624
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area19530 Å2
ΔGint-145 kcal/mol
Surface area83020 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-34 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.911, 115.911, 83.579
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein
Arsenical resistance operon trans-acting repressor


Mass: 11916.065 Da / Num. of mol.: 4 / Fragment: residues 1-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / Gene: BVU_4185 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 magic / References: UniProt: A6L7X2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.94 Å3/Da / Density % sol: 58.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ca(OAc)2 0.1 M MES pH 6.5 20% (w/v) PEG-8000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 21, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 32349 / Num. obs: 32349 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 39.88 Å2 / Rsym value: 0.085 / Net I/σ(I): 15.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.47 / Num. unique all: 1616 / Rsym value: 0.743 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→27.32 Å / SU ML: 0.34 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL / Details: both F+ and F- are used for refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.219 3016 5.05 %random
Rwork0.172 ---
all0.175 59741 --
obs0.175 32257 94.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.017 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4642 Å20 Å20 Å2
2--1.4642 Å20 Å2
3----2.9284 Å2
Refinement stepCycle: LAST / Resolution: 2.1→27.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3213 0 27 487 3727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133355
X-RAY DIFFRACTIONf_angle_d1.3964548
X-RAY DIFFRACTIONf_dihedral_angle_d19.1141262
X-RAY DIFFRACTIONf_chiral_restr0.091538
X-RAY DIFFRACTIONf_plane_restr0.006588
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1-2.1750.33252650.27914939520483
2.175-2.26210.28413070.24195268557587
2.2621-2.3650.26843030.20635452575590
2.365-2.48960.23993030.18495586588993
2.4896-2.64550.2262480.18675791603995
2.6455-2.84950.22433030.18785763606696
2.8495-3.13590.23383190.1885927624698
3.1359-3.58880.21743210.172959756296100
3.5888-4.51820.18063570.135459846251100
4.5182-27.32280.16832900.13296040633099
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined4.10492.34131.66972.30981.30422.52630.8053-0.7374-0.61061.046-0.4615-0.68120.1834-0.2043-0.27220.5007-0.1442-0.23660.31150.18010.363833.171959.859314.812
23.40090.1046-1.66922.6949-0.42162.3251-0.0266-0.19050.21030.34660.01920.0877-0.15570.00830.02090.21220.06780.01640.3615-0.06760.1926
32.9015-0.34891.81412.30250.51184.6380.21290.40660.04140.0919-0.04520.03540.4175-0.2992-0.12160.2204-0.06940.00160.39370.04020.1924
43.3250.54290.90463.18370.1081.80470.05880.07870.0901-0.02990.00150.18860.0115-0.0355-0.04920.1596-0.0082-0.02710.22640.05350.2447
Refinement TLS groupSelection details: chain D

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