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- PDB-1h5w: 2.1A Bacteriophage Phi-29 Connector -

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Basic information

Entry
Database: PDB / ID: 1h5w
Title2.1A Bacteriophage Phi-29 Connector
ComponentsUPPER COLLAR PROTEIN
KeywordsVIRUS / CONNECTOR / PORTAL / SH3-LIKE / HELIX BUNDLE
Function / homology
Function and homology information


viral portal complex / viral procapsid / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / RNA binding
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #30 / Upper collar protein gp10 (connector protein) fold / Upper collar protein gp10 (connector protein) / Bacteriophage PHI-29 conector. Domain 3 / Portal protein Gp10 / Phage Connector (GP10) / Portal protein Gp10 superfamily / Crambin / Serum Albumin; Chain A, Domain 1 / Beta Barrel ...Serum Albumin; Chain A, Domain 1 - #30 / Upper collar protein gp10 (connector protein) fold / Upper collar protein gp10 (connector protein) / Bacteriophage PHI-29 conector. Domain 3 / Portal protein Gp10 / Phage Connector (GP10) / Portal protein Gp10 superfamily / Crambin / Serum Albumin; Chain A, Domain 1 / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesBACTERIOPHAGE PHI-29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGuasch, A. / Pous, J. / Ibarra, B. / Gomis-Ruth, F.X. / Valpuesta, J.M. / Sousa, N. / Carrascosa, J.L. / Coll, M.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Detailed Architecture of a DNA Translocating Machine: The High-Resolution Structure of the Bacteriophage Phi29 Connector Particle.
Authors: Guasch, A. / Pous, J. / Ibarra, B. / Gomis-Ruth, F.X. / Valpuesta, J.M. / Sousa, N. / Carrascosa, J.L. / Coll, M.
History
DepositionMay 28, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jun 28, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Refinement description
Category: atom_site / pdbx_distant_solvent_atoms ...atom_site / pdbx_distant_solvent_atoms / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _software.name / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.pdbx_PDB_helix_id / _struct_conf.pdbx_PDB_helix_length / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.symmetry
Revision 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPPER COLLAR PROTEIN
B: UPPER COLLAR PROTEIN
C: UPPER COLLAR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,2257
Polymers107,7523
Non-polymers4734
Water8,899494
1
A: UPPER COLLAR PROTEIN
B: UPPER COLLAR PROTEIN
C: UPPER COLLAR PROTEIN
hetero molecules

A: UPPER COLLAR PROTEIN
B: UPPER COLLAR PROTEIN
C: UPPER COLLAR PROTEIN
hetero molecules

A: UPPER COLLAR PROTEIN
B: UPPER COLLAR PROTEIN
C: UPPER COLLAR PROTEIN
hetero molecules

A: UPPER COLLAR PROTEIN
B: UPPER COLLAR PROTEIN
C: UPPER COLLAR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)432,89828
Polymers431,00812
Non-polymers1,89116
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,-x+1,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation2_575-x,-y+2,z1
MethodPQS
Unit cell
Length a, b, c (Å)155.340, 155.340, 160.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-585-

HOH

21A-628-

HOH

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Components

#1: Protein UPPER COLLAR PROTEIN / CONNECTOR PROTEIN / LATE PROTEIN GP10


Mass: 35917.293 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTERIOPHAGE PHI-29 (virus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04332
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 52.5 %
Crystal growpH: 8 / Details: 70% MPD, 0.1M TRIS-HCL PH 8
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
170 %MPD1reservoir
20.1 MTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 21, 1999 / Details: TOROIDAL ZERODUR MIRROR
RadiationMonochromator: DIAMOND CRYSTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→42 Å / Num. obs: 327940 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.1 / % possible all: 94.1
Reflection
*PLUS
Num. obs: 56472 / Num. measured all: 327940 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 94.1 % / Rmerge(I) obs: 0.4

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
DMphasing
ARP/wARPphasing
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FOU

1fou


Resolution: 2.1→42 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2861 5 %RANDOM
Rwork0.205 ---
obs0.205 56472 98.8 %-
Solvent computationSolvent model: FLAT / Bsol: 84 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 36.8331 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.231 Å20 Å2
3----0.461 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.1→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6174 0 32 494 6700
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.07
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.51.577
X-RAY DIFFRACTIONc_mcangle_it22.633
X-RAY DIFFRACTIONc_scbond_it22.168
X-RAY DIFFRACTIONc_scangle_it2.53.201
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.308 275 5 %
Rwork0.276 4866 -
obs--91.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2MPD_XPLOR.PARWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMMPD_XPLOR.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.13
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

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