[English] 日本語
Yorodumi
- PDB-1g3p: CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAINS OF BACTERIOPHAGE MINO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g3p
TitleCRYSTAL STRUCTURE OF THE N-TERMINAL DOMAINS OF BACTERIOPHAGE MINOR COAT PROTEIN G3P
ComponentsMINOR COAT PROTEIN
KeywordsVIRAL PROTEIN / MINOR COAT PROTEIN / FILAMENTOUS BACTERIOPHAGE / PHAGE DISPLAY / SELECTIVELY INFECTIVE PHAGES
Function / homology
Function and homology information


viral extrusion / virion attachment to host cell pilus / adhesion receptor-mediated virion attachment to host cell / host cell membrane / viral capsid / entry receptor-mediated virion attachment to host cell / membrane
Similarity search - Function
Minor Coat Protein; domain 2 / Minor Coat Protein; Domain 2 / Phage FD Coat Protein, Membrane penetration domain / Phage FD Coat Protein,Membrane penetration domain / Bacteriophage, G3P, N2-domain superfamily / Attachment protein G3P, N-terminal / Attachment protein G3P, N-terminal domain superfamily / Phage Coat Protein A / Roll / Alpha-Beta Complex ...Minor Coat Protein; domain 2 / Minor Coat Protein; Domain 2 / Phage FD Coat Protein, Membrane penetration domain / Phage FD Coat Protein,Membrane penetration domain / Bacteriophage, G3P, N2-domain superfamily / Attachment protein G3P, N-terminal / Attachment protein G3P, N-terminal domain superfamily / Phage Coat Protein A / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Attachment protein G3P
Similarity search - Component
Biological speciesEnterobacteria phage M13 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS (USING MAD X-RAY DATA) / Resolution: 1.46 Å
AuthorsLubkowski, J. / Hennecke, F. / Pluckthun, A. / Wlodawer, A.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: The structural basis of phage display elucidated by the crystal structure of the N-terminal domains of g3p.
Authors: Lubkowski, J. / Hennecke, F. / Pluckthun, A. / Wlodawer, A.
#1: Journal: Nat.Med. (N.Y.) / Year: 1997
Title: Selectively Infective Phage (Sip) Technology: A Novel Method for in Vivo Selection of Interacting Protein-Ligand Pairs
Authors: Spada, S. / Pluckthun, A.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: The C-Terminal Domain of Tola is the Coreceptor for Filamentous Phage Infection of E. Coli
Authors: Riechmann, L. / Holliger, P.
#3: Journal: Structure / Year: 1997
Title: A Conserved Infection Pathway for Filamentous Bacteriophages is Suggested by the Structure of the Membrane Penetration Domain of the Minor Coat Protein G3P from Phage Fd
Authors: Holliger, P. / Riechmann, L.
History
DepositionDec 22, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 14, 2019Group: Data collection / Category: computing
Revision 1.5Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MINOR COAT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7232
Polymers23,6261
Non-polymers961
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.681, 48.681, 153.222
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21A-302-

HOH

-
Components

#1: Protein MINOR COAT PROTEIN / G3P


Mass: 23626.484 Da / Num. of mol.: 1 / Fragment: TWO N-TERMINAL DOMAINS, N1 AND N2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage M13 (virus) / Genus: Inovirus / Strain: M13MP18 / Cell line: BL21 (DE3) FOR / Gene: 3 / Plasmid: BL21
Cell line (production host): BL21 (DE3), FOR SELENOMETHIONINE-VARIANT DL41 (DE3)
Production host: Escherichia coli (E. coli) / References: UniProt: P69168
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMINOR COAT PROTEIN FROM GENE 3 OF FILAMENTOUS BACTERIOPHAGE M13. THE PHAGE COAT PROTEIN (G3P) ...MINOR COAT PROTEIN FROM GENE 3 OF FILAMENTOUS BACTERIOPHAGE M13. THE PHAGE COAT PROTEIN (G3P) CONSISTS OF THREE DOMAINS. STARTING AT THE N-TERMINUS, THE N1 DOMAIN (67 AMINO ACIDS), THE N2 DOMAIN (131 AMINO ACIDS), AND CT DOMAIN (150 AMINO ACIDS), ARE CONNECTED BY GLYCINE-RICH LINKERS, WHICH CONSIST OF 19 (G1) AND 39 (G2) AMINO ACIDS, RESPECTIVELY. COORDINATES DEPOSITED HERE DESCRIBE ONLY THE TWO DOMAINS (N1 AND N2) OF G3P. THE STRUCTURE OF THE G1 LINKER WAS NOT DETERMINED.
Has protein modificationY
Nonpolymer detailsTRO 21 IS THE OXIDIZED TRP. TRO CARRIES MOST LIKELY AN OXINDOLE SIDE CHAIN (1,3-DIHYDRO-INDOLE-2- ...TRO 21 IS THE OXIDIZED TRP. TRO CARRIES MOST LIKELY AN OXINDOLE SIDE CHAIN (1,3-DIHYDRO-INDOLE-2-ONE). THE OXYGEN ATOM IS BOUND (LIKELY VIA A DOUBLE BOND) TO THE CD1 CARBON. ADDITIONAL EVIDENCE IS PROVIDED BY THE NONPLANARITY OF HYBRIDIZATION OF THE CG CARBON.
Sequence detailsTHE SEQUENCE DIFFERENCES ARE NATURALLY OCCURRING VARIATIONS WHICH DO NOT AFFECT THE FUNCTIONALITY ...THE SEQUENCE DIFFERENCES ARE NATURALLY OCCURRING VARIATIONS WHICH DO NOT AFFECT THE FUNCTIONALITY OF THIS PROTEIN.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 40 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: EQUAL VOLUMES OF THE PROTEIN SOLUTION (10 MG/ML) BUFFERED WITH 50 MM PIPES PH 6.5 AND THE PRECIPITANT (30% PEG 4000, 0.2 M AMMONIUM SULFATE, 2 MM DTT) WERE MIXED AND EQUILIBRATED (IN THE ...Details: EQUAL VOLUMES OF THE PROTEIN SOLUTION (10 MG/ML) BUFFERED WITH 50 MM PIPES PH 6.5 AND THE PRECIPITANT (30% PEG 4000, 0.2 M AMMONIUM SULFATE, 2 MM DTT) WERE MIXED AND EQUILIBRATED (IN THE HANGING DROP SETUP) AGAINST THE PRECIPITANT., vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlN1-N211
20.2 Mammonium sulfate12
330 %(w/v)PEG400012
42 mMDTT12
550 mMPIPES12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 1, 1997 / Details: COLLIMATOR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.46→22 Å / Num. obs: 37511 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.53 % / Rsym value: 0.034 / Net I/σ(I): 27
Reflection shellResolution: 1.46→1.51 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 8.5 / Rsym value: 0.11 / % possible all: 99.2
Reflection
*PLUS
Num. measured all: 282603 / Rmerge(I) obs: 0.034
Reflection shell
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.11

-
Processing

Software
NameVersionClassification
X-PLOR3.1refinement
SCALEPACKdata scaling
SHELX-97model building
SHELX-97refinement
DENZOdata reduction
SHELX-97phasing
RefinementMethod to determine structure: SIRAS (USING MAD X-RAY DATA) / Resolution: 1.46→8 Å / Rfactor Rfree error: 0.0037 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: SEVEN RESIDUES WERE REFINED IN TWO ALTERNATE CONFORMATIONS EACH.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3785 10.2 %RANDOM
Rwork0.187 ---
obs0.187 36895 97.6 %-
Displacement parametersBiso mean: 16.1 Å2
Refinement stepCycle: LAST / Resolution: 1.46→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 20 312 2222
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.584
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.01
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.265
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.341.5
X-RAY DIFFRACTIONx_mcangle_it2.072
X-RAY DIFFRACTIONx_scbond_it2.342
X-RAY DIFFRACTIONx_scangle_it2.072.5
LS refinement shellResolution: 1.46→1.53 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.226 449 11.5 %
Rwork0.221 3906 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.019
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.265

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more