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- PDB-3rb8: Structure of the phage tubulin PhuZ(SeMet)-GDP -

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Basic information

Entry
Database: PDB / ID: 3rb8
TitleStructure of the phage tubulin PhuZ(SeMet)-GDP
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / Tubulin
Function / homology
Function and homology information


establishment of localization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / host cell cytoplasm / GTPase activity / GTP binding / identical protein binding
Similarity search - Function
Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Phage tubulin-like protein
Similarity search - Component
Biological speciesPseudomonas phage 201phi2-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsAgard, D.A. / Pogliano, J. / Kraemer, J.A. / Erb, M.L. / Waddling, C.A. / Montabana, E.A. / Wang, H. / Nguyen, K. / Pham, S.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: A phage tubulin assembles dynamic filaments by an atypical mechanism to center viral DNA within the host cell.
Authors: Kraemer, J.A. / Erb, M.L. / Waddling, C.A. / Montabana, E.A. / Zehr, E.A. / Wang, H. / Nguyen, K. / Pham, D.S. / Agard, D.A. / Pogliano, J.
History
DepositionMar 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4583
Polymers34,9911
Non-polymers4682
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.981, 76.062, 92.758
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein


Mass: 34990.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage 201phi2-1 (virus) / Gene: 201phi2-1p059 / Production host: Escherichia coli (E. coli) / References: UniProt: B3FK34
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 6000, 0.1M Hepes, 0.5M Ammonium Acetate, 0.05M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97201, 0.97969
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2009
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.972011
20.979691
ReflectionResolution: 2.4→46.379 Å / Num. all: 25117 / Num. obs: 23023 / % possible obs: 91.67 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→46.379 Å / SU ML: 0.34
Isotropic thermal model: Isotropic with TLS refinement with eleven groups
σ(F): 1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2373 1867 9.92 %random
Rwork0.1633 ---
obs0.1706 18830 95.32 %-
all-23023 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.427 Å2 / ksol: 0.313 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.2866 Å2-0 Å20 Å2
2---3.2448 Å2-0 Å2
3---8.5313 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 29 14 2462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082487
X-RAY DIFFRACTIONf_angle_d1.1413385
X-RAY DIFFRACTIONf_dihedral_angle_d14.645922
X-RAY DIFFRACTIONf_chiral_restr0.07404
X-RAY DIFFRACTIONf_plane_restr0.004435
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.6-2.67050.34151230.24911181118185
2.6705-2.7490.36431340.25371203120388
2.749-2.83770.35051330.23361223122390
2.8377-2.93920.34271380.21581253125391
2.9392-3.05680.28151360.21251271127194
3.0568-3.19590.31341470.20611332133297
3.1959-3.36430.3241510.19351360136099
3.3643-3.57510.2491540.18381346134698
3.5751-3.8510.20441570.151329132999
3.851-4.23830.22441410.13451376137699
4.2383-4.8510.16781500.109513481348100
4.851-6.10950.19691470.145113781378100
6.1095-46.38640.20291560.148713631363100
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)
10.4376-0.11730.18350.29890.05340.3723-0.2409-0.02260.09660.3750.0152-0.2567-0.49870.1391-0.03960.63710.0575-0.38660.2404-0.03870.62714.43154.7768-1.7166
20.25740.1223-0.40370.9652-0.99811.3724-0.67390.09221.0339-0.1421-0.2885-0.2168-0.84330.1541-0.33631.06420.1336-0.62230.6127-0.18591.012615.33781.25782.774
30.3878-0.17160.18491.2592-0.61570.3549-0.1435-0.31460.17260.76550.3376-0.1374-0.3441-0.0830.05420.65240.1498-0.13450.45470.01150.3375.8419-7.54690.4418
41.1826-0.14240.39511.32560.34430.3878-0.07610.15020.0520.48650.1355-0.0110.32790.097-0.02910.36540.0489-0.08380.22770.01660.24025.6162-10.2373-9.1494
50.05760.17880.09590.9841-0.39751.3251-0.2244-0.1420.0535-0.0748-0.0012-0.36850.03840.13370.10990.4147-0.06090.04160.45720.06340.36914.4398-4.8005-16.0528
60.0472-0.22270.07541.0535-0.35350.3613-0.1019-0.05180.23320.0428-0.1802-0.7389-0.14970.2202-0.33890.8194-0.0155-0.4026-0.01330.17210.64513.30847.4044-13.46
70.3312-0.13260.34711.56030.47850.6330.0613-0.4202-0.1868-0.1545-0.16491.04360.0081-0.41570.0630.3522-0.02590.05560.60250.03970.6554-12.403-4.6901-12.2029
80.5-0.0394-0.41660.9815-0.16730.4134-0.71290.43770.3982-0.7006-0.24930.088-0.77160.1361-1.12840.57460.0381-0.62640.35610.12980.6366-12.15233.536-23.9418
91.3228-0.51-0.55421.2904-0.3410.5104-0.4024-0.07950.4734-0.34680.07510.5228-0.575-0.5213-0.53980.49660.1734-0.28250.4976-0.06770.6915-13.23215.7334-18.2082
100.41770.0838-0.48260.99210.36681.5117-0.37940.48840.1639-0.19780.2387-0.5352-0.00320.24270.05680.4508-0.11260.02260.6621-0.09050.400115.431-13.4639-24.709
112.3849-1.1648-0.18542.9910.13040.5958-0.13960.3501-0.54660.90780.18460.54870.439-0.11960.02860.5422-0.0496-0.07520.51830.06720.502649.9479-20.4309-13.0733
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:32)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 33:59)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 60:94)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 95:143)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 144:160)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 161:178)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 179:214)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 215:238)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 239:271)
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 272:294)
11X-RAY DIFFRACTION11CHAIN A AND (RESSEQ 295:315)

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