[English] 日本語
Yorodumi
- PDB-1mqk: Crystal structure of the unliganded Fv-fragment of the anti-cytoc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mqk
TitleCrystal structure of the unliganded Fv-fragment of the anti-cytochrome C oxidase antibody 7E2
Components
  • antibody 7E2 FV fragment, heavy chain
  • antibody 7E2 FV fragment, light chain
KeywordsIMMUNE SYSTEM / antibody / membrane protein / cytochrome C oxidase / high-resolution structure
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / adaptive immune response / immune response / extracellular region
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig kappa chain V-V region MOPC 149 / Ig heavy chain V region 5-84
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsEssen, L.-O. / Harrenga, A. / Ostermeier, C. / Michel, H.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: 1.3 A X-ray structure of an antibody Fv fragment used for induced membrane-protein crystallization.
Authors: Essen, L.O. / Harrenga, A. / Ostermeier, C. / Michel, H.
#1: Journal: Proteins / Year: 1995
Title: Crystals of an antibody Fv fragment against an integral membrane protein diffracting to 1.28 resolution
Authors: Ostermeier, C. / Essen, L.-O. / Michel, H.
#2: Journal: Nat.Struct.Biol. / Year: 1995
Title: Fv fragment-mediated crystallization of the membrane protein bacterial cytochrome C oxidase
Authors: Ostermeier, C. / Iwata, S. / Ludwig, B. / Michel, H.
#3: Journal: Nature / Year: 1995
Title: Structure at 2.8 resolution of cytochrome C oxidase from Paracoccus denitrificans
Authors: Iwata, S. / Ostermeier, C. / Ludwig, B. / Michel, H.
#4: Journal: J.Biol.Chem. / Year: 1999
Title: The cytochrome C oxidase from Paracoccus denitrificans does not change the metal center upon reduction
Authors: Harrenga, A. / Michel, H.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Structure at 2.7 resolution of the Paracoccus denitrificans two-subunit cytochrome C oxidase complexed with an antibody Fv fragment
Authors: Ostermeier, C. / Harrenga, A. / Ermler, U. / Michel, H.
History
DepositionSep 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Nov 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE ACCORDING TO THE AUTHOR, THE SEQUENCE FOR THE HEAVY AND LIGHT CHAINS OF ANTIBODY 7E2 HAS ...SEQUENCE ACCORDING TO THE AUTHOR, THE SEQUENCE FOR THE HEAVY AND LIGHT CHAINS OF ANTIBODY 7E2 HAS NOT BEEN DEPOSITED IN ANY SEQUENCE DATABASE. SOME SEQUENCE INFORMATION IS PRESENT IN PDB ENTRY 1QLE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: antibody 7E2 FV fragment, light chain
H: antibody 7E2 FV fragment, heavy chain


Theoretical massNumber of molelcules
Total (without water)27,5862
Polymers27,5862
Non-polymers00
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-16 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.436, 56.045, 99.846
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody antibody 7E2 FV fragment, light chain


Mass: 13260.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pASK68 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P01636
#2: Antibody antibody 7E2 FV fragment, heavy chain


Mass: 14324.923 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pASK68 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P18525
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 6
Details: sodium phosphate, pH 6.0, MICRODIALYSIS, temperature 277K
Crystal
*PLUS
Density % sol: 53 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein11
2100 mMsodium phosphate11pH6.0

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 12, 1993 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.28→22.5 Å / Num. obs: 64251 / % possible obs: 85.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.4 / Net I/σ(I): 28.6
Reflection shellResolution: 1.28→1.31 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 5.2 / % possible all: 63.4
Reflection
*PLUS
Num. measured all: 178789 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 63.4 %

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
X-PLORmodel building
SHELXLrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QLE

1qle


Resolution: 1.28→8 Å / Isotropic thermal model: anisotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Used weighted full matrix least squares procedure of SHELX-93 to generate model. Only isotropic model provided
RfactorNum. reflectionSelection details
Rfree0.196 1922 random
Rwork0.136 --
all0.136 64005 -
obs0.136 64005 -
Displacement parametersBiso mean: 22.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.1 Å / Luzzati sigma a obs: 0.07 Å
Refinement stepCycle: LAST / Resolution: 1.28→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 0 318 2193
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d2.28
X-RAY DIFFRACTIONs_bond_d0.021
X-RAY DIFFRACTIONo_dihedral_angle_d28.1
Software
*PLUS
Name: SHELXL / Version: 93 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / % reflection Rfree: 4 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.28
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg28.1

+
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