[English] 日本語
Yorodumi
- PDB-2g3p: STRUCTURE OF THE N-TERMINAL TWO DOMAINS OF THE INFECTIVITY PROTEI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2g3p
TitleSTRUCTURE OF THE N-TERMINAL TWO DOMAINS OF THE INFECTIVITY PROTEIN G3P OF FILAMENTOUS PHAGE FD
ComponentsINFECTIVITY PROTEIN G3P
KeywordsVIRAL PROTEIN / INFECTION / FILAMENTOUS PHAGE / PILUS BINDING / BETA BARREL / CONFORMATIONAL CHANGE
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 fd (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.9 Å
AuthorsHolliger, P. / Williams, R.L.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of the two N-terminal domains of g3p from filamentous phage fd at 1.9 A: evidence for conformational lability.
Authors: Holliger, P. / Riechmann, L. / Williams, R.L.
History
DepositionOct 27, 1998Processing site: BNL
Revision 1.0Jul 19, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: INFECTIVITY PROTEIN G3P
B: INFECTIVITY PROTEIN G3P


Theoretical massNumber of molelcules
Total (without water)49,1512
Polymers49,1512
Non-polymers00
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-17 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.220, 78.250, 62.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.865487, -0.02829, -0.500131), (-0.043205, -0.990468, 0.130792), (-0.499064, 0.134807, 0.856015)
Vector: 58.732, 52.105, 12.066)

-
Components

#1: Protein INFECTIVITY PROTEIN G3P


Mass: 24575.518 Da / Num. of mol.: 2 / Fragment: N-TERMINAL 2-DOMAIN FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage fd (virus) / Genus: Inovirus / Species: Enterobacteria phage M13 / Plasmid: PUC119 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / Variant (production host): LAC / References: UniProt: P03661
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 56 %
Crystal growpH: 6.2 / Details: pH 6.2
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
24.3 Msodium formate1reservoir
30.1 Msodium cacodylate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.947
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 1, 1998 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.947 Å / Relative weight: 1
ReflectionResolution: 1.6→13.8 Å / Num. obs: 81474 / % possible obs: 99.7 % / Redundancy: 5.6 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 4.7
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.45 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 58927 / % possible obs: 99.8 % / Num. measured all: 343352 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→13 Å / SU B: 3.5 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1499 3.1 %RANDOM
Rwork0.26 ---
obs-47624 99.7 %-
Displacement parametersBiso mean: 40 Å2
Refinement stepCycle: LAST / Resolution: 1.9→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 0 303 3463
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.02
X-RAY DIFFRACTIONp_angle_d0.0240.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0230.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0522
X-RAY DIFFRACTIONp_mcangle_it1.7443
X-RAY DIFFRACTIONp_scbond_it1.1212
X-RAY DIFFRACTIONp_scangle_it1.8543
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.299 / Rfactor Rwork: 0.257
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.006
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.5

+
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