[English] 日本語
Yorodumi
- PDB-4ouo: anti-Bla g 1 scFv -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ouo
Titleanti-Bla g 1 scFv
Componentsanti Bla g 1 scFv
KeywordsIMMUNE SYSTEM / cockroach allergen / IgG / scFv antibody fragment / Bla g 1
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMueller, G.A. / Ankney, J.A. / Glesner, J. / Khurana, T. / Edwards, L.L. / Pedersen, L.C. / Perera, L. / Slater, J.E. / Pomes, A. / London, R.E.
CitationJournal: Mol.Immunol. / Year: 2014
Title: Characterization of an anti-Bla g 1 scFv: Epitope mapping and cross-reactivity.
Authors: Mueller, G.A. / Ankney, J.A. / Glesner, J. / Khurana, T. / Edwards, L.L. / Pedersen, L.C. / Perera, L. / Slater, J.E. / Pomes, A. / London, R.E.
History
DepositionFeb 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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: anti Bla g 1 scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8236
Polymers24,5251
Non-polymers2985
Water2,828157
1
A: anti Bla g 1 scFv
hetero molecules

A: anti Bla g 1 scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,64712
Polymers49,0502
Non-polymers59710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area5340 Å2
ΔGint-150 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.500, 51.100, 44.900
Angle α, β, γ (deg.)90.00, 105.00, 90.00
Int Tables number5
Space group name H-MC121
DetailsScFv biological unit is a monomer but due to a too short linker between the two IgG domains, the N-terminal domain of one molecule forms the biological scFv structure with the C-terminal domain of another molecule (and vise-versa) that is related by a 180 degree rotation.

-
Components

#1: Antibody anti Bla g 1 scFv


Mass: 24524.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pDEST566 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.8M Ammonium Sulfate, 100mM NaCl, 50mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 2, 2012
RadiationMonochromator: Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 19780 / Num. obs: 19780 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 22.45 Å2 / Rsym value: 0.048 / Net I/σ(I): 18.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 758 / Rsym value: 0.176 / % possible all: 72

-
Processing

Software
NameVersionClassification
SERGUIdata collection
MLPHAREphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UX9

3ux9


Resolution: 1.8→29.654 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1912 965 5 %Random
Rwork0.165 ---
obs0.1663 19291 92.13 %-
all-19780 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→29.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 13 157 1806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111704
X-RAY DIFFRACTIONf_angle_d1.3582323
X-RAY DIFFRACTIONf_dihedral_angle_d11.539578
X-RAY DIFFRACTIONf_chiral_restr0.081262
X-RAY DIFFRACTIONf_plane_restr0.006302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.8950.28361070.19982038X-RAY DIFFRACTION72
1.895-2.01370.25571320.19022483X-RAY DIFFRACTION88
2.0137-2.16910.2111370.18062654X-RAY DIFFRACTION95
2.1691-2.38730.22021450.17862736X-RAY DIFFRACTION96
2.3873-2.73260.21471420.18232761X-RAY DIFFRACTION97
2.7326-3.4420.19941500.16342795X-RAY DIFFRACTION98
3.442-29.65830.14921520.14572859X-RAY DIFFRACTION98

+
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