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- PDB-2vve: Crystal structure of the stem and receptor binding domain of the ... -

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Entry
Database: PDB / ID: 2vve
TitleCrystal structure of the stem and receptor binding domain of the spike protein P1 from bacteriophage PM2
ComponentsSPIKE PROTEIN P1
KeywordsVIRAL PROTEIN / VIRAL STEM-RECEPTOR BINDING DOMAIN
Function / homologyJelly Rolls - #770 / Jelly Rolls - #720 / virion component / Jelly Rolls / Sandwich / Mainly Beta / Spike protein P1
Function and homology information
Biological speciesPSEUDOALTEROMONAS PHAGE PM2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_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.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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SPIKE PROTEIN P1
B: SPIKE PROTEIN P1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3797
Polymers57,1832
Non-polymers1965
Water9,710539
1
A: SPIKE PROTEIN P1
hetero molecules

A: SPIKE PROTEIN P1
hetero molecules

A: SPIKE PROTEIN P1
hetero molecules

A: SPIKE PROTEIN P1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,66812
Polymers114,3664
Non-polymers3028
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area8570 Å2
ΔGint-15.8 kcal/mol
Surface area53000 Å2
MethodPQS
2
B: SPIKE PROTEIN P1
hetero molecules

B: SPIKE PROTEIN P1
hetero molecules

B: SPIKE PROTEIN P1
hetero molecules

B: SPIKE PROTEIN P1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,84716
Polymers114,3664
Non-polymers48112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455y-1,-x,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area8380 Å2
ΔGint-17.5 kcal/mol
Surface area54040 Å2
MethodPQS
Unit cell
Length a, b, c (Å)107.894, 107.894, 44.171
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11A-2063-

HOH

21B-2048-

HOH

31B-2067-

HOH

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Components

#1: Protein SPIKE PROTEIN P1 / P1-RECEPTOR BINDING PROTEIN


Mass: 28591.408 Da / Num. of mol.: 2 / Fragment: STEM-RECEPTOR BINDING DOMAIN, RESIDUES 82-335
Source method: isolated from a genetically manipulated source
Details: CLONED FRAGMENT STARTS AT RESIDUE 82 AND STOPS AT RESIDUE 335
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.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 539 / 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: 45.4 %
Description: THE ELECTRON DENSITY MAP FOR THE STEM DOMAIN WAS GREATLY IMPROVED BY USING BUSTER PROGRAM IN THE EARLY REFINEMENT CYCLES
Crystal growpH: 8
Details: 7.3MG/ML (IN 150MM NACL, 20MM TRIS PH 7.5, 10MM CACL2),20%(W/V) PEG6K,100MM TRIS PH 8, 200MM LICL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9185
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 30, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9185 Å / Relative weight: 1
ReflectionResolution: 1.77→23 Å / Num. obs: 47548 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 30.2
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.8 / % possible all: 71.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VVD

2vvd


Resolution: 1.77→23 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.082 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DESPITE HAVING TWO MOLECULES IN THE ASU THE RESPECTIVE STEM DOMAINS FLEX WITH DIFFERENT ANGLES RELATIVE TO THE RECEPTOR DOMAIN. THEREFORE NO STRICT NCS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2423 5.1 %RANDOM
Rwork0.173 ---
obs0.176 45122 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.77→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3966 0 5 539 4510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224081
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0971.9455555
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8635512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25824.471208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52215655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6371526
X-RAY DIFFRACTIONr_chiral_restr0.0750.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023188
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1810.21676
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22791
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2443
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.2125
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.249
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.807102571
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.732204076
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.045201705
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.438401473
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: 1.77→1.81 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 110
Rwork0.242 2426
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)
10.97860.06610.22320.7189-0.130.71430.0141-0.00360.09650.0875-0.0403-0.058-0.10450.0320.02620.064-0.012-0.02770.03340.00150.0176.86314.60233.952
22.17830.0965-0.06471.1830.1522.0860.0097-0.09220.2094-0.1157-0.0398-0.0801-0.06430.03330.03010.04530.00270.00490.0047-0.00710.01043.62136.0161.707
30.14320.4829-0.24482.0789-1.7142.17060.0039-0.0162-0.03150.1232-0.0809-0.1074-0.15030.04930.0770.03480.0151-0.0170.04670.00460.01154.15327.4119.345
40.9512-0.35060.30270.7669-0.32290.81-0.00120.05440.02650.0527-0.0262-0.17010.05410.15170.02740.04110.0012-0.00680.07390.01340.0159-37.89251.191-25.082
52.13680.60331.21122.33672.06563.3545-0.0188-0.30490.1087-0.0057-0.16740.1375-0.071-0.42360.1862-0.00780.0453-0.0160.0833-0.05-0.0388-21.2340.446.963
61.52670.15611.13990.01730.08861.4482-0.135-0.14030.20360.0005-0.0076-0.0078-0.1525-0.04490.14270.05590.0433-0.03020.0842-0.05550.0061-22.10342.5591.86
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A84 - 168
2X-RAY DIFFRACTION2A169 - 306
3X-RAY DIFFRACTION3A307 - 335
4X-RAY DIFFRACTION4B85 - 170
5X-RAY DIFFRACTION5B171 - 263
6X-RAY DIFFRACTION6B264 - 335

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