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- PDB-3pqi: Crystal structure of the bacteriophage phi92 membrane-piercing pr... -

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Basic information

Entry
Database: PDB / ID: 3pqi
TitleCrystal structure of the bacteriophage phi92 membrane-piercing protein gp138
Componentsgene product 138
KeywordsVIRAL PROTEIN / Beta-Helix / OB-Fold / Phage Baseplate / Iron-Binding / Cell membrane piercing
Function / homology
Function and homology information


Chondroitinase Ac; Chain A, domain 3 - #20 / Chondroitinase Ac; Chain A, domain 3 / Phage protein Gp138 N-terminal domain / Phage protein Gp138 N-terminal domain / Gp5 N-terminal domain / Vgr protein, OB-fold domain superfamily / Other non-globular / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacteriophage phi92 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.642 Å
AuthorsBrowning, C. / Shneider, M. / Leiman, P.G.
CitationJournal: Structure / Year: 2012
Title: Phage pierces the host cell membrane with the iron-loaded spike.
Authors: Browning, C. / Shneider, M.M. / Bowman, V.D. / Schwarzer, D. / Leiman, P.G.
History
DepositionNov 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: gene product 138
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9803
Polymers25,8851
Non-polymers952
Water70339
1
A: gene product 138
hetero molecules

A: gene product 138
hetero molecules

A: gene product 138
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9399
Polymers77,6543
Non-polymers2856
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area22010 Å2
ΔGint-182 kcal/mol
Surface area24240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.144, 65.144, 329.375
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-246-

FE

21A-272-

HOH

31A-280-

HOH

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Components

#1: Protein gene product 138


Mass: 25884.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage phi92 (virus) / Production host: Escherichia coli (E. coli) / Strain (production host): 834 (DE3) / References: UniProt: I7HXF9*PLUS
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.652.66
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2911vapor diffusion, hanging drop810 mg/ml 10% - 12% PEG 2K 100mM - 200mM MgCl2 100mM Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
2912vapor diffusion, hanging drop7.510 mg/ml 10% - 12% PEG 2K 250mM KCl 50mM Tris pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 7, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.64→55.61 Å / Num. all: 8322 / Num. obs: 8304 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 10.5 % / Biso Wilson estimate: 44.9 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.093 / Net I/σ(I): 18.4
Reflection shellResolution: 2.642→2.78 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.517 / Rsym value: 0.469 / % possible all: 98.1

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.642→55.607 Å / SU ML: 0.19 / σ(F): 1.94 / Phase error: 26.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2501 415 5.01 %
Rwork0.2107 --
obs0.2127 8279 99.16 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.104 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso mean: 66.22 Å2
Baniso -1Baniso -2Baniso -3
1--10.4162 Å20 Å20 Å2
2---10.4162 Å20 Å2
3---20.8324 Å2
Refinement stepCycle: LAST / Resolution: 2.642→55.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1481 0 2 39 1522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041508
X-RAY DIFFRACTIONf_angle_d0.7942048
X-RAY DIFFRACTIONf_dihedral_angle_d12.711540
X-RAY DIFFRACTIONf_chiral_restr0.054244
X-RAY DIFFRACTIONf_plane_restr0.003265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.642-3.02430.28011340.23772549X-RAY DIFFRACTION99
3.0243-3.81020.29651370.20252591X-RAY DIFFRACTION99
3.8102-55.61890.22031440.2072724X-RAY DIFFRACTION99
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)
10.19670.02050.07590.37620.38710.3554-0.0013-0.54060.2650.20550.38660.2148-0.4045-0.14450.00070.6584-0.04870.14810.583-0.01650.7345-20.05232.2521134.8102
21.1496-0.05780.42540.0988-0.13610.24860.15140.34840.1473-0.1262-0.40210.4743-0.0401-0.0499-0.07490.5775-0.03550.15420.3571-0.14210.8705-11.15836.9667130.1767
30.7560.0511-0.09890.4443-0.55120.65830.0605-0.16390.15840.4788-0.18070.02430.0911-0.0231-0.00010.402-0.05730.06390.4063-0.01460.6382-7.339-1.1173124.5565
40.6985-0.2114-0.32780.6705-0.06420.59030.06160.1775-0.1403-0.15750.02250.09070.1705-0.2222-0.0010.2729-0.0282-0.08260.2747-0.01450.2337-2.2206-4.985981.9601
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 22:58)
2X-RAY DIFFRACTION2chain 'A' and (resseq 59:70)
3X-RAY DIFFRACTION3chain 'A' and (resseq 71:144)
4X-RAY DIFFRACTION4chain 'A' and (resseq 145:243)

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