[English] 日本語
Yorodumi
- PDB-3gm0: Anti-methamphetamine single chain Fv in complex with MDMA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gm0
TitleAnti-methamphetamine single chain Fv in complex with MDMA
Componentsanti-methamphetamine single chain Fv
KeywordsIMMUNE SYSTEM / anti-methamphetamine antibody / single chain Fv / Therapeutic antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-B41
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsCelikel, R. / Peterson, E.C. / Owens, M. / Varughese, K.I.
CitationJournal: Protein Sci. / Year: 2009
Title: Crystal structures of a therapeutic single chain antibody in complex with two drugs of abuse-Methamphetamine and 3,4-methylenedioxymethamphetamine.
Authors: Celikel, R. / Peterson, E.C. / Owens, S.M. / Varughese, K.I.
History
DepositionMar 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: anti-methamphetamine single chain Fv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9832
Polymers27,7891
Non-polymers1931
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.720, 64.806, 48.322
Angle α, β, γ (deg.)90.000, 98.970, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody anti-methamphetamine single chain Fv


Mass: 27789.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: IgG / Plasmid: pPICZ-alpha / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H
#2: Chemical ChemComp-B41 / (2S)-1-(1,3-benzodioxol-5-yl)-N-methylpropan-2-amine / 3,4 methylenedioxy-n-methylamphetamine / MDMA / Ecstasy


Mass: 193.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE PROTEIN WAS CRYSTALLIZED AS A FUSION PROTEIN WHERE TWO CHAINS, CHAIN H AND CHAIN L, WERE FUSED ...THE PROTEIN WAS CRYSTALLIZED AS A FUSION PROTEIN WHERE TWO CHAINS, CHAIN H AND CHAIN L, WERE FUSED TOGETHER INTO ONE CHAIN USING A 15-RESIDUE LINKER. THE SEQUENCE OF THE LINKER IS: GGGGS GGGGS GGGGS. IN ADDITION, THERE IS A FLAG EPITOPE AT THE N-TERMINAL AND THERE IS A HIS-TAG AT THE C-TERMINAL. PLEASE NOTE THAT THE AMINO ACID NUMBERING IN THIS PDB FILE A SEQUENTIAL NUMBERING OF THE SCFV6H4 SINGLE CHAIN ANTIBODY AMINO ACIDS DUE TO PDB POLICY. PLEASE SEE THE ORIGINAL MANUSCRIPT FOR THE MORE COMMON KABAT AMINO ACID NUMBERING SCHEME OF THE HEAVY AND LIGHT CHAIN RESIDUES. PLEASE USE THE CORRELATION PROVIDED BELOW FOR CONVERTING TO KABAT NUMBERING SCHEME USED IN OUR MANUSCRIPT. PDB NUMBER (PUBLICATION NUMBER): A9 (H1), A90 (H82), A91 (H82A), A92 (H82B), A93 (H82C), A94 (H93), A110 (H99), A111 (H100A), A112 (H100B), A113 (H100C), A114 (H101), A141 (L1), A167 (L27), A168 (L27A), A169 (L28), A247 (L106), A248 (L106A), A249 (L107), HOH 505 (OW(5)), HOH 506 (OW(6))

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.35 %
Crystal growTemperature: 287 K / Method: vapor diffusion / pH: 8.3
Details: 1.15M sodium Citrate, 0.28M Imidazole malate, pH 8.3, VAPOR DIFFUSION, temperature 287K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2008 / Details: single crystal bent monochromator
RadiationMonochromator: single crystal bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.4→32.4 Å / Num. all: 8316 / Num. obs: 8316 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Redundancy: 3.75 % / Rsym value: 0.045
Reflection shellResolution: 2.4→2.58 Å / Redundancy: 3.7 % / Rsym value: 0.21 / % possible all: 99.5

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.4→15 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.271 592 7.1 %
Rwork0.214 --
obs-8316 99.8 %
Solvent computationBsol: 66.944 Å2
Displacement parametersBiso max: 82.68 Å2 / Biso mean: 39.042 Å2 / Biso min: 16.72 Å2
Baniso -1Baniso -2Baniso -3
1-16.17 Å20 Å21.382 Å2
2---11.194 Å20 Å2
3----4.976 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1797 0 14 77 1888
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.4-2.670.3451630.311X-RAY DIFFRACTION2092
2.67-2.930.3121030.251X-RAY DIFFRACTION1505
2.93-3.350.3141150.219X-RAY DIFFRACTION1512
3.35-4.210.2621040.195X-RAY DIFFRACTION1501
4.21-150.2191050.186X-RAY DIFFRACTION1541
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param
X-RAY DIFFRACTION3mdma.param

+
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