[English] 日本語
Yorodumi
- PDB-6y1m: Crystal structure of the paraoxon-modified A.17 antibody FAB frag... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y1m
TitleCrystal structure of the paraoxon-modified A.17 antibody FAB fragment - L47K mutant
Components
  • FAB A.17 L47K mutant HEAVY CHAIN
  • FAB A.17 L47K mutant Light CHAIN
KeywordsIMMUNE SYSTEM / QM/MM computation / designed biocatalysts / bioscavengers / phosphoryl transfer / organophosphorus agents
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DIETHYL PHOSPHONATE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChatziefthimiou, S. / Mokrushina, Y. / Smirnov, I. / Gabibov, A. / Wilmanns, M.
Funding support Germany, Russian Federation, 2items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research05K14YEB Germany
Russian Foundation for Basic ResearchRFMEFI60414X0069 Russian Federation
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Multiscale computation delivers organophosphorus reactivity and stereoselectivity to immunoglobulin scavengers.
Authors: Mokrushina, Y.A. / Golovin, A.V. / Smirnov, I.V. / Chatziefthimiou, S.D. / Stepanova, A.V. / Bobik, T.V. / Zalevsky, A.O. / Zlobin, A.S. / Konovalov, K.A. / Terekhov, S.S. / Stepanov, A.V. / ...Authors: Mokrushina, Y.A. / Golovin, A.V. / Smirnov, I.V. / Chatziefthimiou, S.D. / Stepanova, A.V. / Bobik, T.V. / Zalevsky, A.O. / Zlobin, A.S. / Konovalov, K.A. / Terekhov, S.S. / Stepanov, A.V. / Pipiya, S.O. / Shamborant, O.G. / Round, E. / Belogurov Jr., A.A. / Bourenkov, G. / Makarov, A.A. / Wilmanns, M. / Xie, J. / Blackburn, G.M. / Gabibov, A.G. / Lerner, R.A.
History
DepositionFeb 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: FAB A.17 L47K mutant HEAVY CHAIN
L: FAB A.17 L47K mutant Light CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1603
Polymers54,0222
Non-polymers1381
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-16 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.942, 66.979, 66.083
Angle α, β, γ (deg.)90.00, 107.54, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody FAB A.17 L47K mutant HEAVY CHAIN


Mass: 27415.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Komagataella phaffii GS115 (fungus)
#2: Antibody FAB A.17 L47K mutant Light CHAIN


Mass: 26606.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Komagataella phaffii GS115 (fungus)
#3: Chemical ChemComp-DEP / DIETHYL PHOSPHONATE


Mass: 138.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11O3P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growMethod: vapor diffusion, hanging drop / Details: 0.1M ADA, pH 7.5 0.17M MgCl2 20% PEG 6K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→28.51 Å / Num. obs: 29559 / % possible obs: 98.85 % / Redundancy: 4.1 % / CC1/2: 0.998 / Net I/σ(I): 11.1
Reflection shellResolution: 2→2.072 Å / Num. unique obs: 2923 / CC1/2: 0.512

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xzc

2xzc


Resolution: 2→28.51 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.22
RfactorNum. reflection% reflection
Rfree0.2302 1503 5.09 %
Rwork0.1822 --
obs0.1847 29555 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→28.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3230 0 8 192 3430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123376
X-RAY DIFFRACTIONf_angle_d1.3484587
X-RAY DIFFRACTIONf_dihedral_angle_d12.9441199
X-RAY DIFFRACTIONf_chiral_restr0.058519
X-RAY DIFFRACTIONf_plane_restr0.007586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.06460.35051120.28462550X-RAY DIFFRACTION99
2.0646-2.13840.40081290.2632561X-RAY DIFFRACTION99
2.1384-2.2240.31291430.25212526X-RAY DIFFRACTION99
2.224-2.32510.29981300.23222528X-RAY DIFFRACTION99
2.3251-2.44770.25421690.21852536X-RAY DIFFRACTION99
2.4477-2.60090.25931420.21182518X-RAY DIFFRACTION99
2.6009-2.80160.24151430.19962522X-RAY DIFFRACTION99
2.8016-3.08330.24681250.18212555X-RAY DIFFRACTION98
3.0833-3.52880.21451320.16672584X-RAY DIFFRACTION99
3.5288-4.44350.20111470.13582567X-RAY DIFFRACTION99
4.4435-29.57520.16011310.15362605X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6358-0.21240.10533.1409-0.23674.10790.0040.2782-0.3531-0.1115-0.12570.01840.2543-0.20490.08970.1663-0.00580.00990.2033-0.02620.19490.3729-3.1461-1.4137
22.61510.8616-1.22592.7808-1.8453.98760.0321-0.16-0.04270.1091-0.06430.0910.02530.10640.02910.2363-0.0266-0.02560.1847-0.01010.225310.4081-7.645328.0132
33.4960.1969-1.19341.7601-0.04093.95960.14970.25570.24720.0080.01270.1058-0.2289-0.1286-0.12480.17420.0370.02160.18940.0180.2201-17.06234.991210.1147
45.4120.34991.71440.6093-0.08421.6949-0.0038-0.1770.04060.09740.03230.02470.0054-0.1036-0.01380.2260.0054-0.00420.1632-0.00380.16938.03044.480137.4854
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain H and resid 1:117)
2X-RAY DIFFRACTION2(chain H and resid 118:222)
3X-RAY DIFFRACTION3(chain L and resid 2:107)
4X-RAY DIFFRACTION4(chain L and resid 108:216)

+
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