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- PDB-3qr7: Crystal structure of the C-terminal fragment of the bacteriophage... -

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Basic information

Entry
Database: PDB / ID: 3qr7
TitleCrystal structure of the C-terminal fragment of the bacteriophage P2 membrane-piercing protein gpV
ComponentsBaseplate assembly protein V
KeywordsVIRAL PROTEIN / Beta-Helix / OB-Fold / Phage Baseplate / Iron-Binding / Cell membrane piercing / Tail spike
Function / homology
Function and homology information


virus tail, baseplate / viral tail assembly / symbiont genome entry into host cell via pore formation in plasma membrane / entry receptor-mediated virion attachment to host cell / metal ion binding
Similarity search - Function
Phage spike trimer / Phage spike trimer / Phage baseplate assembly protein V/Gp45 / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily
Similarity search - Domain/homology
Biological speciesEnterobacteria phage P2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.94 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
DepositionFeb 17, 2011Deposition 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
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Baseplate assembly protein V
B: Baseplate assembly protein V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8729
Polymers23,5862
Non-polymers2867
Water8,377465
1
A: Baseplate assembly protein V
hetero molecules

A: Baseplate assembly protein V
hetero molecules

A: Baseplate assembly protein V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,84315
Polymers35,3803
Non-polymers46312
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 area22610 Å2
ΔGint-205 kcal/mol
Surface area13500 Å2
MethodPISA
2
B: Baseplate assembly protein V
hetero molecules

B: Baseplate assembly protein V
hetero molecules

B: Baseplate assembly protein V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,77412
Polymers35,3803
Non-polymers3949
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area22140 Å2
ΔGint-164 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.069, 49.069, 463.896
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-1-

CL

21A-212-

CA

31A-2-

FE

41B-2-

CL

51B-212-

CA

61B-1-

FE

71B-381-

HOH

81B-388-

HOH

91B-401-

HOH

101B-403-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Baseplate assembly protein V / GpV


Mass: 11793.225 Da / Num. of mol.: 2 / Fragment: C-terminal domain (UNP residues 97-211)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P2 (virus) / Gene: V / Production host: Escherichia coli (E. coli) / References: UniProt: P31340

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Non-polymers , 5 types, 472 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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 (%)
12.2846.01
2
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mg/mL protein, 30% PEE 797, 0.3 M ammonium sulfate, 0.1 M MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.8
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2009
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.94→27.33 Å / Num. obs: 141144 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.063 / Rsym value: 0.058 / Net I/σ(I): 16.6
Reflection shellResolution: 0.94→0.99 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 5.8 / Num. unique all: 20367 / Rsym value: 0.256 / % possible all: 99.9

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Processing

Software
NameVersionClassification
RemDAqdata collection
SHELXC/D/Emodel building
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXC/D/Ephasing
RefinementMethod to determine structure: SAD / Resolution: 0.94→27.327 Å / SU ML: 0.07 / σ(F): 1.36 / Phase error: 7.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.112 2827 2 %
Rwork0.1023 --
obs0.1025 141095 99.78 %
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 110.84 Å2 / ksol: 0.464 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9682 Å20 Å20 Å2
2---0.9682 Å20 Å2
3---1.9363 Å2
Refinement stepCycle: LAST / Resolution: 0.94→27.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 7 465 2122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172029
X-RAY DIFFRACTIONf_angle_d1.9912822
X-RAY DIFFRACTIONf_dihedral_angle_d11.753786
X-RAY DIFFRACTIONf_chiral_restr0.12342
X-RAY DIFFRACTIONf_plane_restr0.013382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.94-0.95620.18551370.16426836X-RAY DIFFRACTION100
0.9562-0.97360.15891190.14726821X-RAY DIFFRACTION100
0.9736-0.99230.15891370.13426839X-RAY DIFFRACTION100
0.9923-1.01260.12851590.11416835X-RAY DIFFRACTION100
1.0126-1.03460.11261540.1056828X-RAY DIFFRACTION100
1.0346-1.05870.11861370.0916852X-RAY DIFFRACTION100
1.0587-1.08510.08181460.08166842X-RAY DIFFRACTION100
1.0851-1.11450.09061450.07596890X-RAY DIFFRACTION100
1.1145-1.14730.0881460.07476841X-RAY DIFFRACTION100
1.1473-1.18430.08891390.07366838X-RAY DIFFRACTION100
1.1843-1.22660.09011450.0736935X-RAY DIFFRACTION100
1.2266-1.27570.09481350.07156838X-RAY DIFFRACTION100
1.2757-1.33380.08951200.07626933X-RAY DIFFRACTION100
1.3338-1.40410.10061490.0786900X-RAY DIFFRACTION100
1.4041-1.49210.091220.07926940X-RAY DIFFRACTION100
1.4921-1.60730.09471300.08216944X-RAY DIFFRACTION100
1.6073-1.7690.09691520.096961X-RAY DIFFRACTION100
1.769-2.02490.10641520.09336994X-RAY DIFFRACTION100
2.0249-2.55090.11211590.10667038X-RAY DIFFRACTION100
2.5509-27.33880.14981440.14837363X-RAY DIFFRACTION99

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