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- PDB-4dwl: Avd molecule from Bordetella bacteriophage DGR -

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Basic information

Entry
Database: PDB / ID: 4dwl
TitleAvd molecule from Bordetella bacteriophage DGR
ComponentsBbp7
Keywordsnucleic acid binding protein / pentameric four helix bundle / Accessory variability determinant from Bordetella bacteriophage diversity generating retroelements / Reverse Transcriptase / phosphate binding protein
Function / homology23S rRNA-intervening sequence / Bbp7-like / 23S rRNA-intervening sequence superfamily / de novo design (two linked rop proteins) / Up-down Bundle / Mainly Alpha / PHOSPHATE ION / Bbp7
Function and homology information
Biological speciesBordetella phage BPP-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.69 Å
AuthorsGhosh, P. / Al-Ayyoubi, M.
CitationJournal: Structure / Year: 2013
Title: Structure of the essential diversity-generating retroelement protein bAvd and its functionally important interaction with reverse transcriptase.
Authors: Alayyoubi, M. / Guo, H. / Dey, S. / Golnazarian, T. / Brooks, G.A. / Rong, A. / Miller, J.F. / Ghosh, P.
History
DepositionFeb 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Bbp7
B: Bbp7
E: Bbp7
C: Bbp7
D: Bbp7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1396
Polymers75,0445
Non-polymers951
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-61 kcal/mol
Surface area25480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.317, 63.072, 105.295
Angle α, β, γ (deg.)90.00, 103.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'B' and ((resseq 64:66))
211chain 'A' and ((resseq 64:66))
311chain 'E' and ((resseq 64:66))
411chain 'C' and ((resseq 64:66))
511chain 'D' and ((resseq 64:66))
112chain 'C' and ((resseq 14:16))
212chain 'E' and ((resseq 14:16))

NCS ensembles :
ID
1
2
DetailsFive Avd molecules in the assymetric unit arranged around a five fold axis of symmetry

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Components

#1: Protein
Bbp7


Mass: 15008.841 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella phage BPP-1 (virus) / Gene: bbp7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q775D7
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 3350, 0.2M magnesium chloride, 0.4M barium chloride, 0.1M Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97941, 0.97950, 0.97630
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2009
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979411
20.97951
30.97631
ReflectionResolution: 2.5→50 Å / Num. obs: 43542 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.093
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.5-2.54166.4
2.54-2.59171.7
2.59-2.64176.7
2.64-2.69178.5
2.69-2.75183.4
2.75-2.82187.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.69→42.91 Å / SU ML: 0.34 / σ(F): 1.94 / Phase error: 27.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 1854 5.07 %
Rwork0.1944 --
obs0.197 36535 96.99 %
all-43482 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.476 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-28.6253 Å20 Å2-11.3751 Å2
2---16.4608 Å20 Å2
3----12.9613 Å2
Refinement stepCycle: LAST / Resolution: 2.69→42.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4328 0 5 61 4394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094416
X-RAY DIFFRACTIONf_angle_d1.1695955
X-RAY DIFFRACTIONf_dihedral_angle_d15.5081637
X-RAY DIFFRACTIONf_chiral_restr0.071676
X-RAY DIFFRACTIONf_plane_restr0.005737
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B22X-RAY DIFFRACTIONPOSITIONAL0.008
12A22X-RAY DIFFRACTIONPOSITIONAL0.008
13E22X-RAY DIFFRACTIONPOSITIONAL0.008
14C22X-RAY DIFFRACTIONPOSITIONAL0.009
15D22X-RAY DIFFRACTIONPOSITIONAL0.008
21C24X-RAY DIFFRACTIONPOSITIONAL0.013
22E24X-RAY DIFFRACTIONPOSITIONAL0.013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.78620.33181470.24812981X-RAY DIFFRACTION84
2.7862-2.89770.3461750.24823276X-RAY DIFFRACTION91
2.8977-3.02950.28961790.23483417X-RAY DIFFRACTION95
3.0295-3.18920.28071880.22283603X-RAY DIFFRACTION100
3.1892-3.38890.25192040.20443551X-RAY DIFFRACTION100
3.3889-3.65050.25262030.20223573X-RAY DIFFRACTION100
3.6505-4.01760.19661730.16663566X-RAY DIFFRACTION100
4.0176-4.59840.20381760.1573611X-RAY DIFFRACTION100
4.5984-5.79120.23631930.19433559X-RAY DIFFRACTION100
5.7912-42.9150.2312160.18833544X-RAY DIFFRACTION99

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