[English] 日本語
Yorodumi
- PDB-6dwa: Structure of the 4497 Antibody Fab fragment bound to a Staphyloco... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dwa
TitleStructure of the 4497 Antibody Fab fragment bound to a Staphylococcus aureus wall techoic acid analog
Components
  • 4497 Fab Heavy Chain
  • 4497 Fab Light Chain
KeywordsIMMUNE SYSTEM / Antibody / Fab / wall teichoic acid / WTA / Staphylococcus aureus
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-HD4
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.922 Å
AuthorsFong, R. / Lupardus, P.J.
CitationJournal: MAbs / Year: 2018
Title: Structural investigation of human S. aureus-targeting antibodies that bind wall teichoic acid.
Authors: Fong, R. / Kajihara, K. / Chen, M. / Hotzel, I. / Mariathasan, S. / Hazenbos, W.L.W. / Lupardus, P.J.
History
DepositionJun 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4497 Fab Light Chain
B: 4497 Fab Heavy Chain
H: 4497 Fab Heavy Chain
L: 4497 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,3546
Polymers104,4834
Non-polymers8712
Water7,692427
1
A: 4497 Fab Light Chain
B: 4497 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6773
Polymers52,2422
Non-polymers4351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-24 kcal/mol
Surface area18830 Å2
MethodPISA
2
H: 4497 Fab Heavy Chain
L: 4497 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6773
Polymers52,2422
Non-polymers4351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-25 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.681, 114.443, 156.364
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody 4497 Fab Light Chain


Mass: 26485.666 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 4497 Fab Heavy Chain


Mass: 25755.895 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: Sugar ChemComp-HD4 / 4-O-[2-acetamido-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol / 4-O-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol / 4-O-[2-acetamido-2-deoxy-beta-D-glucosyl]-1-O-phosphono-D-ribitol / 4-O-[2-acetamido-2-deoxy-D-glucosyl]-1-O-phosphono-D-ribitol / 4-O-[2-acetamido-2-deoxy-glucosyl]-1-O-phosphono-D-ribitol


Type: D-saccharide / Mass: 435.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H26NO13P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.16M Calcium Acetate, 0.08 M Sodium Cacodylate, pH 6.5, 14.4% PEG8000, and 20% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 87337 / % possible obs: 99.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 20.2
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8494 / % possible all: 98

-
Processing

Software
NameVersionClassification
PHENIX1.7_648refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KVN

4kvn


Resolution: 1.922→42.563 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.18
RfactorNum. reflection% reflection
Rfree0.2352 4243 5.05 %
Rwork0.2069 --
obs0.2084 84098 95.87 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 40.596 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.6531 Å20 Å2-0 Å2
2--1.1151 Å20 Å2
3----5.7682 Å2
Refinement stepCycle: LAST / Resolution: 1.922→42.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6585 0 56 427 7068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076844
X-RAY DIFFRACTIONf_angle_d1.0979311
X-RAY DIFFRACTIONf_dihedral_angle_d13.3052453
X-RAY DIFFRACTIONf_chiral_restr0.0731053
X-RAY DIFFRACTIONf_plane_restr0.0051193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9219-1.94370.3871030.28872236X-RAY DIFFRACTION81
1.9437-1.96660.31271260.26942356X-RAY DIFFRACTION87
1.9666-1.99060.30531160.26372462X-RAY DIFFRACTION88
1.9906-2.01580.32151470.24612417X-RAY DIFFRACTION89
2.0158-2.04230.2911380.24882450X-RAY DIFFRACTION90
2.0423-2.07030.2661370.24122444X-RAY DIFFRACTION91
2.0703-2.09990.27881210.23552538X-RAY DIFFRACTION92
2.0999-2.13120.2851350.22542620X-RAY DIFFRACTION94
2.1312-2.16450.28391310.21942592X-RAY DIFFRACTION94
2.1645-2.20.26111230.21232622X-RAY DIFFRACTION94
2.2-2.23790.24821360.21012586X-RAY DIFFRACTION95
2.2379-2.27860.241270.21222642X-RAY DIFFRACTION95
2.2786-2.32240.25041520.22632636X-RAY DIFFRACTION97
2.3224-2.36980.27661730.22272691X-RAY DIFFRACTION97
2.3698-2.42140.30431330.21292683X-RAY DIFFRACTION98
2.4214-2.47770.21451320.21032731X-RAY DIFFRACTION98
2.4777-2.53960.24671460.21192696X-RAY DIFFRACTION98
2.5396-2.60830.26851390.21832749X-RAY DIFFRACTION99
2.6083-2.6850.22551560.21572739X-RAY DIFFRACTION99
2.685-2.77170.27471330.20892777X-RAY DIFFRACTION99
2.7717-2.87070.25421490.21672753X-RAY DIFFRACTION100
2.8707-2.98560.23621650.20762738X-RAY DIFFRACTION100
2.9856-3.12150.24591670.20672774X-RAY DIFFRACTION100
3.1215-3.2860.2141460.19422788X-RAY DIFFRACTION100
3.286-3.49180.2171410.19122800X-RAY DIFFRACTION100
3.4918-3.76120.21791570.19242811X-RAY DIFFRACTION100
3.7612-4.13950.21361440.19042818X-RAY DIFFRACTION100
4.1395-4.73780.19461460.17192852X-RAY DIFFRACTION100
4.7378-5.96650.19581590.1962854X-RAY DIFFRACTION100
5.9665-42.57320.23561650.22783000X-RAY DIFFRACTION100

+
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