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- PDB-2vvd: Crystal structure of the receptor binding domain of the spike pro... -

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Basic information

Entry
Database: PDB / ID: 2vvd
TitleCrystal structure of the receptor binding domain of the spike protein P1 from bacteriophage PM2
ComponentsSPIKE PROTEIN P1
KeywordsVIRAL PROTEIN / VIRAL RECEPTOR BINDING DOMAIN
Function / homologyJelly Rolls - #720 / Phage PM2 spike protein P1 / Spike protein P1, first jelly-roll domain / Spike protein P1, second jelly-roll domain / virion component / Jelly Rolls / Sandwich / Mainly Beta / Spike protein P1
Function and homology information
Biological speciesPSEUDOALTEROMONAS PHAGE PM2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.26 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 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPIKE PROTEIN P1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2463
Polymers20,1661
Non-polymers802
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.645, 49.055, 72.177
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 SPIKE PROTEIN P1 / P1-RECEPTOR BINDING PROTEIN


Mass: 20165.787 Da / Num. of mol.: 1 / Fragment: RECEPTOR BINDING DOMAIN, RESIDUES 159-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOALTEROMONAS PHAGE PM2 (virus) / Plasmid: POPINF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q9XJR3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFRAGMENT CLONED STARTS AT RESIDUE 159 AND STOPS AT 335

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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: 1.94 Å3/Da / Density % sol: 36.94 % / Description: NONE
Crystal growpH: 7.5
Details: 7.4MG/ML PROTEIN (IN 150MM NACL AND 20MM TRIS PH 7.5), 20%(W/V) PEG3350, 200MM CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97912,0.90499
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 22, 2005 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979121
20.904991
ReflectionResolution: 2.26→21.6 Å / Num. obs: 6935 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Biso Wilson estimate: 14.65 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 46.5
Reflection shellResolution: 2.26→2.33 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 27.7 / % possible all: 52.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.26→21.6 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.886 / SU B: 5.422 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.587 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 369 5.4 %RANDOM
Rwork0.169 ---
obs0.172 6521 89.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2--0.23 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.26→21.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1284 0 2 169 1455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221319
X-RAY DIFFRACTIONr_bond_other_d0.0010.02861
X-RAY DIFFRACTIONr_angle_refined_deg0.9661.951797
X-RAY DIFFRACTIONr_angle_other_deg0.7732099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.215163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87524.62767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.20515205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.924156
X-RAY DIFFRACTIONr_chiral_restr0.0620.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021496
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02277
X-RAY DIFFRACTIONr_nbd_refined0.1810.2219
X-RAY DIFFRACTIONr_nbd_other0.1880.2905
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2652
X-RAY DIFFRACTIONr_nbtor_other0.0780.2685
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2150
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1190.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.190.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2591.5832
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.45521313
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8873560
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.254.5483
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.26→2.32 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.235 12
Rwork0.16 261

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