[English] 日本語
Yorodumi
- PDB-4ptt: Crystal Structure of anti-23F strep Fab C05 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ptt
TitleCrystal Structure of anti-23F strep Fab C05
Components
  • Antibody pn132p2C05, heavy chain
  • Antibody pn132p2C05, light chain
KeywordsIMMUNE SYSTEM / Antibody / Fab fragment / 23F / Rhamnose
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBryson, S. / Risnes, L. / Damgupta, S. / Thomson, C.A. / Smith, K. / Schrader, J.W. / Pai, E.F.
CitationJournal: J. Immunol. / Year: 2016
Title: Structures of Preferred Human IgV Genes-Based Protective Antibodies Identify How Conserved Residues Contact Diverse Antigens and Assign Source of Specificity to CDR3 Loop Variation.
Authors: Bryson, S. / Thomson, C.A. / Risnes, L.F. / Dasgupta, S. / Smith, K. / Schrader, J.W. / Pai, E.F.
History
DepositionMar 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antibody pn132p2C05, light chain
B: Antibody pn132p2C05, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5326
Polymers48,2632
Non-polymers2694
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-26 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.140, 48.760, 80.000
Angle α, β, γ (deg.)90.00, 120.82, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-780-

HOH

-
Components

#1: Antibody Antibody pn132p2C05, light chain


Mass: 23534.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle
#2: Antibody Antibody pn132p2C05, heavy chain


Mass: 24728.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M Na Acetate, 20% PEG 1500, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 9, 2013 / Details: Osmic VariMaxTM
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→35.7 Å / Num. all: 40827 / Num. obs: 40261 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.82 % / Rsym value: 0.0324 / Net I/σ(I): 44.7
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 25.3 / Num. unique all: 3099 / Rsym value: 0.0586 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry HIE

Resolution: 1.8→35.7 Å / SU ML: 0.16 / σ(F): 0 / Phase error: 18.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1962 2024 5.03 %Random
Rwork0.171 ---
obs0.1723 40216 98.56 %-
all-40804 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 18 332 3636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073387
X-RAY DIFFRACTIONf_angle_d1.1524598
X-RAY DIFFRACTIONf_dihedral_angle_d13.5241201
X-RAY DIFFRACTIONf_chiral_restr0.05515
X-RAY DIFFRACTIONf_plane_restr0.005596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.20581360.15782638X-RAY DIFFRACTION97
1.845-1.89490.2341340.15952682X-RAY DIFFRACTION97
1.8949-1.95060.22181460.1642727X-RAY DIFFRACTION98
1.9506-2.01360.16761650.15682628X-RAY DIFFRACTION98
2.0136-2.08550.18831320.16132734X-RAY DIFFRACTION98
2.0855-2.16890.20931380.16182700X-RAY DIFFRACTION99
2.1689-2.26760.21351340.17252742X-RAY DIFFRACTION99
2.2676-2.38710.2181650.1792707X-RAY DIFFRACTION99
2.3871-2.53650.21221380.18782772X-RAY DIFFRACTION99
2.5365-2.73210.21171690.19172726X-RAY DIFFRACTION100
2.7321-3.00670.21611480.19142762X-RAY DIFFRACTION100
3.0067-3.44080.2211460.17992745X-RAY DIFFRACTION99
3.4408-4.33150.18131370.16232779X-RAY DIFFRACTION98
4.3315-25.22370.13721360.15522850X-RAY DIFFRACTION99

+
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