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- PDB-2vvf: Crystal structure of the major capsid protein P2 from Bacteriopha... -

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Basic information

Entry
Database: PDB / ID: 2vvf
TitleCrystal structure of the major capsid protein P2 from Bacteriophage PM2
ComponentsMAJOR CAPSID PROTEIN P2
KeywordsVIRAL PROTEIN / DOUBLE JELLY-ROLL VIRAL CAPSID
Function / homology
Function and homology information


viral capsid, major subunit
Similarity search - Function
Jelly Rolls - #730 / Viral coat protein P2, N-terminal / : / Viral coat protein P2 N-terminal domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major capsid protein P2 / Major capsid protein P2
Similarity search - Component
Biological speciesPSEUDOALTEROMONAS PHAGE PM2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAbrescia, N.G.A. / Grimes, J.M. / Kivela, H.K. / Assenberg, R. / Sutton, G.C. / Butcher, S.J. / Bamford, J.K.H. / Bamford, D.H. / Stuart, D.I.
CitationJournal: Mol.Cell / Year: 2008
Title: Insights Into Virus Evolution and Membrane Biogenesis from the Structure of the Marine Lipid-Containing Bacteriophage Pm2.
Authors: Abrescia, N.G.A. / Grimes, J.M. / Kivela, H.K. / Assenberg, R. / Sutton, G.C. / Butcher, S.J. / Bamford, J.K.H. / Bamford, D.H. / Stuart, D.I.
History
DepositionJun 6, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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_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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAJOR CAPSID PROTEIN P2
B: MAJOR CAPSID PROTEIN P2
C: MAJOR CAPSID PROTEIN P2
D: MAJOR CAPSID PROTEIN P2
E: MAJOR CAPSID PROTEIN P2
F: MAJOR CAPSID PROTEIN P2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,64312
Polymers181,4026
Non-polymers2406
Water3,261181
1
A: MAJOR CAPSID PROTEIN P2
B: MAJOR CAPSID PROTEIN P2
C: MAJOR CAPSID PROTEIN P2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8216
Polymers90,7013
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-38.2 kcal/mol
Surface area37390 Å2
MethodPQS
2
D: MAJOR CAPSID PROTEIN P2
E: MAJOR CAPSID PROTEIN P2
F: MAJOR CAPSID PROTEIN P2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8216
Polymers90,7013
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-40.7 kcal/mol
Surface area37340 Å2
MethodPQS
Unit cell
Length a, b, c (Å)163.990, 77.570, 127.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-2040-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99728, -0.07329, -0.00776), (-0.04303, -0.49366, -0.86859), (0.05983, 0.86656, -0.49547)16.76786, 612.76147, 403.86151
2given(0.99799, -0.04533, 0.04432), (-0.06111, -0.50212, 0.86264), (-0.01685, -0.86361, -0.50388)-8.38102, -47.67023, 738.02698
3given(0.99726, 0.07399, -0.00069), (-0.07398, 0.99725, 0.00487), (0.00105, -0.0048, 0.99999)-92.42001, -16.08124, 58.86206
4given(0.99, -0.12112, -0.07234), (-0.12233, -0.48153, -0.86785), (0.07028, 0.86802, -0.49153)-28.00676, 597.50079, 456.86597
5given(0.99106, -0.07431, 0.11084), (-0.13324, -0.50526, 0.85262), (-0.00735, -0.85976, -0.51065)-107.14326, -58.54114, 795.00244

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Components

#1: Protein
MAJOR CAPSID PROTEIN P2 / P2 MAJOR CAPSID PROTEIN


Mass: 30233.723 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) PSEUDOALTEROMONAS PHAGE PM2 (virus) / References: UniProt: Q9XJR7, UniProt: P15794*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Description: THE DIFFRACTION IMAGES CONTAINED MULTIPLE LATTICES. TWO OF THEM WERE CONSISTENTLY INDEXED AND INTEGRATED THEN MERGED TO PRODUCE THE FINAL DATASET. THE P2 STRUCTURE HAS BEEN SOLVED USING ...Description: THE DIFFRACTION IMAGES CONTAINED MULTIPLE LATTICES. TWO OF THEM WERE CONSISTENTLY INDEXED AND INTEGRATED THEN MERGED TO PRODUCE THE FINAL DATASET. THE P2 STRUCTURE HAS BEEN SOLVED USING AS STARTING MODEL THE ELECTRON DENSITY OF A P2 TRIMER CUT OUT FROM THE AVERAGED PM2 PHAGE DENSITY. FOR DETAILS SEE ARTICLES AND PDB ENTRY FOR PHAGE PM2.
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97848
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 10, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97848 Å / Relative weight: 1
ReflectionResolution: 2.5→41 Å / Num. obs: 54091 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Redundancy: 30.4 % / Rmerge(I) obs: 0.26 / Net I/σ(I): 16.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 2 / % possible all: 70.7

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Processing

Software
NameVersionClassification
BUSTER-TNT5.6.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→41 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: WE IMPOSED 6-FOLD NCS AS RESTRAINT DURING REFINEMENT IN BUSTER. SOME RESIDUES WERE NOT INCLUDED IN THE NCS DUE TO THE DIFFERENT SIDE-CHAIN CONFORMATION. THE NCS PROVIDED BELOW HAVE BEEN USED ...Details: WE IMPOSED 6-FOLD NCS AS RESTRAINT DURING REFINEMENT IN BUSTER. SOME RESIDUES WERE NOT INCLUDED IN THE NCS DUE TO THE DIFFERENT SIDE-CHAIN CONFORMATION. THE NCS PROVIDED BELOW HAVE BEEN USED AS CONSTRAINTS IN THE STRUCTURE SOLUTION AND AS RESTRAINTS IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2576 2731 5.1 %RANDOM
Rwork0.2399 ---
obs0.2408 51087 94 %-
Refinement stepCycle: LAST / Resolution: 2.5→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12738 0 6 181 12925

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