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- PDB-4hv0: Structure and Function of AvtR, a Novel Transcriptional Regulator... -

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Basic information

Entry
Database: PDB / ID: 4hv0
TitleStructure and Function of AvtR, a Novel Transcriptional Regulator from a Hyperthermophilic Archaeal Lipothrixvirus
ComponentsAvtR
KeywordsTRANSCRIPTION / VIRAL PROTEIN / ribbon-helix-helix / DNA
Function / homologyRibbon-helix-helix protein, copG family / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / regulation of DNA-templated transcription / Orthogonal Bundle / Mainly Alpha / Putative regulatory protein
Function and homology information
Biological speciesAcidianus filamentous virus 6
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsPeixeiro, N. / Keller, J. / Collinet, B. / Leulliot, N. / Campanacci, V. / Cortez, D. / Cambillau, C. / Nitta, K.R. / Vincentelli, R. / Forterre, P. ...Peixeiro, N. / Keller, J. / Collinet, B. / Leulliot, N. / Campanacci, V. / Cortez, D. / Cambillau, C. / Nitta, K.R. / Vincentelli, R. / Forterre, P. / Prangishvili, D. / Sezonov, G. / van Tilbeurgh, H.
CitationJournal: J.Virol. / Year: 2013
Title: Structure and Function of AvtR, a Novel Transcriptional Regulator from a Hyperthermophilic Archaeal Lipothrixvirus.
Authors: Peixeiro, N. / Keller, J. / Collinet, B. / Leulliot, N. / Campanacci, V. / Cortez, D. / Cambillau, C. / Nitta, K.R. / Vincentelli, R. / Forterre, P. / Prangishvili, D. / Sezonov, G. / van Tilbeurgh, H.
History
DepositionNov 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AvtR
B: AvtR
C: AvtR
D: AvtR


Theoretical massNumber of molelcules
Total (without water)52,0874
Polymers52,0874
Non-polymers00
Water1,17165
1
A: AvtR


Theoretical massNumber of molelcules
Total (without water)13,0221
Polymers13,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AvtR


Theoretical massNumber of molelcules
Total (without water)13,0221
Polymers13,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: AvtR


Theoretical massNumber of molelcules
Total (without water)13,0221
Polymers13,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: AvtR


Theoretical massNumber of molelcules
Total (without water)13,0221
Polymers13,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.153, 59.550, 84.039
Angle α, β, γ (deg.)90.00, 102.76, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A2 - 99
2010B2 - 99
1020A2 - 99
2020C2 - 99
1030A2 - 99
2030D2 - 99
1040B2 - 99
2040C2 - 99
1050B2 - 99
2050D2 - 99
1060C2 - 100
2060D2 - 100

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
AvtR


Mass: 13021.695 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidianus filamentous virus 6 / Gene: gp29 / Plasmid: pET9 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) pLysS / References: UniProt: A7WKI3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22-27% PEG4000, 0.1 M HEPES, pH 7.5, 5-10% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.971 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationMonochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.971 Å / Relative weight: 1
ReflectionResolution: 2.6→81.92 Å / Num. all: 15055 / Num. obs: 14095 / % possible obs: 98.8 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 3 / Redundancy: 14 % / Net I/σ(I): 20.9
Reflection shellResolution: 2.6→2.668 Å / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 3 / % possible all: 90.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→81.92 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.219 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.845 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25832 753 5.1 %RANDOM
Rwork0.21147 ---
obs0.21383 14095 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 59.87 Å2
Baniso -1Baniso -2Baniso -3
1-3.48 Å20 Å2-0.56 Å2
2---1.2 Å20 Å2
3----2.52 Å2
Refinement stepCycle: LAST / Resolution: 2.6→81.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3106 0 0 65 3171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023139
X-RAY DIFFRACTIONr_bond_other_d0.0070.022343
X-RAY DIFFRACTIONr_angle_refined_deg1.7642.0174174
X-RAY DIFFRACTIONr_angle_other_deg1.54135710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1755365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.94223.382136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.63915675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7091528
X-RAY DIFFRACTIONr_chiral_restr0.0920.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023263
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02621
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A33340.16
12B33340.16
21A33590.14
22C33590.14
31A34770.14
32D34770.14
41B34450.11
42C34450.11
51B33230.18
52D33230.18
61C33010.16
62D33010.16
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 42 -
Rwork0.285 865 -
obs--85.49 %

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