[English] 日本語
Yorodumi
- PDB-5xaj: Structural mimicry of the dengue virus envelope glycoprotein reve... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xaj
TitleStructural mimicry of the dengue virus envelope glycoprotein revealed by the crystallographic study of an idiotype-anti-idiotype Fab complex.
Components
  • (Fab E1 heavy ...) x 2
  • Fab E1 light chain
  • FabHM14c10 heavy chain
  • FabHM14c10 light chain
KeywordsIMMUNE SYSTEM / Complex / Antibody / Anti-idiotype
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWong, Y.H. / Goh, B.C. / Lescar, J.
Funding support Singapore, 3items
OrganizationGrant numberCountry
MOERG62/12 Singapore
NMRCNMRC/CBRG/0028/2014 Singapore
SMARTSMART Scholarship Singapore
CitationJournal: J. Virol. / Year: 2017
Title: Structural mimicry of the dengue virus envelope glycoprotein revealed by the crystallographic study of an idiotype-anti-idiotype Fab complex
Authors: Wong, Y.H. / Goh, B.C. / Lim, S.Y. / Teo, E.W. / Lim, A.P.C. / Dedon, P.C. / Hanson, B.J. / MacAry, P.A. / Lescar, J.
History
DepositionMar 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FabHM14c10 heavy chain
B: FabHM14c10 light chain
C: Fab E1 light chain
D: Fab E1 light chain
E: Fab E1 heavy chain
F: Fab E1 heavy chain
H: FabHM14c10 heavy chain
L: FabHM14c10 light chain


Theoretical massNumber of molelcules
Total (without water)186,0298
Polymers186,0298
Non-polymers00
Water23,2931293
1
A: FabHM14c10 heavy chain
B: FabHM14c10 light chain


Theoretical massNumber of molelcules
Total (without water)47,4522
Polymers47,4522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-29 kcal/mol
Surface area19980 Å2
MethodPISA
2
C: Fab E1 light chain
E: Fab E1 heavy chain


Theoretical massNumber of molelcules
Total (without water)45,4032
Polymers45,4032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-23 kcal/mol
Surface area20640 Å2
MethodPISA
3
D: Fab E1 light chain
F: Fab E1 heavy chain
L: FabHM14c10 light chain


Theoretical massNumber of molelcules
Total (without water)69,1773
Polymers69,1773
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-23 kcal/mol
Surface area20520 Å2
MethodPISA
4
H: FabHM14c10 heavy chain


Theoretical massNumber of molelcules
Total (without water)23,9971
Polymers23,9971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-27 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.300, 47.590, 220.759
Angle α, β, γ (deg.)90.00, 93.43, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Antibody , 5 types, 8 molecules AHBLCDEF

#1: Antibody FabHM14c10 heavy chain


Mass: 23997.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: ESCHERICHIA COLI (E. coli)
#2: Antibody FabHM14c10 light chain


Mass: 23455.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: ESCHERICHIA COLI (E. coli)
#3: Antibody Fab E1 light chain


Mass: 22948.373 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: ESCHERICHIA COLI (E. coli)
#4: Antibody Fab E1 heavy chain


Mass: 22454.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: ESCHERICHIA COLI (E. coli)
#5: Antibody Fab E1 heavy chain


Mass: 22773.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: ESCHERICHIA COLI (E. coli)

-
Non-polymers , 1 types, 1293 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1293 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.57 % / Description: Plate
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Ammonium acetate, Bis Tris Propane pH 5.5, PEG 10,000

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.0428 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0428 Å / Relative weight: 1
ReflectionResolution: 2.5→52.67 Å / Num. obs: 84640 / % possible obs: 99.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 45.15 Å2 / Net I/σ(I): 6.5
Reflection shellResolution: 2.5→2.64 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 12224 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.93 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.893 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.335 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.38 / SU Rfree Blow DPI: 0.252 / SU Rfree Cruickshank DPI: 0.246
RfactorNum. reflection% reflectionSelection details
Rfree0.239 4183 4.94 %RANDOM
Rwork0.185 ---
obs0.187 84627 99.7 %-
Displacement parametersBiso mean: 36.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.8733 Å20 Å2-1.2126 Å2
2---4.4598 Å20 Å2
3---6.3331 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: 1 / Resolution: 2.5→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13020 0 0 1311 14331
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113354HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2818203HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4333SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes261HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1963HARMONIC5
X-RAY DIFFRACTIONt_it13354HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.69
X-RAY DIFFRACTIONt_other_torsion19.42
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1762SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14710SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 312 5.09 %
Rwork0.226 5817 -
all0.23 6129 -
obs--99.71 %

+
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