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- PDB-4ru3: Crystal structure of the cell puncturing protein Orf41 from Pseud... -

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Basic information

Entry
Database: PDB / ID: 4ru3
TitleCrystal structure of the cell puncturing protein Orf41 from Pseudomonas phage SN
Componentspuncturing protein gp41
KeywordsCELL INVASION / gp41 / membrane translocation / phage baseplate / Cell puncturing device
Function / homologyPhage protein Gp138 N-terminal domain / Phage protein Gp138 N-terminal domain / Vgr protein, OB-fold domain superfamily / metal ion binding / : / Putative baseplate protein
Function and homology information
Biological speciesPseudomonas phage SN (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.172 Å
AuthorsBrowning, C. / Shneider, M.M. / Leiman, P.G.
CitationJournal: To be Published
Title: Crystal structure of the cell puncturing protein Orf41 from Pseudomonas phage SN
Authors: Browning, C. / Shneider, M.M. / Leiman, P.G.
History
DepositionNov 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.2Sep 25, 2019Group: Data collection / Database references / Structure summary
Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.3Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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_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

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Assembly

Deposited unit
A: puncturing protein gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2744
Polymers24,0861
Non-polymers1883
Water5,585310
1
A: puncturing protein gp41
hetero molecules

A: puncturing protein gp41
hetero molecules

A: puncturing protein gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,82212
Polymers72,2583
Non-polymers5649
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area25660 Å2
ΔGint-177 kcal/mol
Surface area22860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.540, 84.540, 84.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-301-

FE

21A-302-

CA

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Components

#1: Protein puncturing protein gp41 / Putative baseplate protein


Mass: 24085.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage SN (virus) / Gene: ORF41
Plasmid: pEE3, pET-23 derivative (TEV cleavage site after His-tag)
Production host: Escherichia coli (E. coli) / Strain (production host): B834/DE3 / References: UniProt: B7VFI6
#2: Chemical ChemComp-FE / FE (III) ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5
Details: 21% PEG 10K, 0.1M Ammonium acetate, 0.1M Bis-Tris pH 5.0, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 5, 2011
RadiationMonochromator: Si(111) Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.17→34.513 Å / Num. all: 67585 / Num. obs: 67579 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 17.7 % / Rmerge(I) obs: 0.068 / Rsym value: 0.071 / Net I/σ(I): 23.1
Reflection shellResolution: 1.17→1.24 Å / Redundancy: 17.8 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 8.8 / Num. unique all: 9781 / Rsym value: 0.309 / % possible all: 100

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.172→34.513 Å / SU ML: 0.07 / σ(F): 0.08 / Phase error: 11.31 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1499 2009 2.98 %RANDOM
Rwork0.1343 ---
obs0.1348 67339 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.172→34.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1578 0 8 310 1896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131806
X-RAY DIFFRACTIONf_angle_d1.5852485
X-RAY DIFFRACTIONf_dihedral_angle_d14.397680
X-RAY DIFFRACTIONf_chiral_restr0.106276
X-RAY DIFFRACTIONf_plane_restr0.009340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.172-1.20130.15241390.12444559X-RAY DIFFRACTION99
1.2013-1.23380.13671430.11674587X-RAY DIFFRACTION99
1.2338-1.27010.14561430.11494606X-RAY DIFFRACTION99
1.2701-1.31110.16221370.11414628X-RAY DIFFRACTION99
1.3111-1.3580.14361420.10474641X-RAY DIFFRACTION100
1.358-1.41240.12521430.10214641X-RAY DIFFRACTION100
1.4124-1.47660.12341450.09724667X-RAY DIFFRACTION100
1.4766-1.55450.12341420.0954639X-RAY DIFFRACTION100
1.5545-1.65190.11961390.10264658X-RAY DIFFRACTION100
1.6519-1.77940.12331460.11194695X-RAY DIFFRACTION100
1.7794-1.95850.14511440.11994687X-RAY DIFFRACTION100
1.9585-2.24180.13771480.12844686X-RAY DIFFRACTION100
2.2418-2.82430.17571460.15814764X-RAY DIFFRACTION100
2.8243-34.52830.16411520.16154872X-RAY DIFFRACTION100

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