[English] 日本語
Yorodumi
- PDB-4m61: Crystal structure of unliganded anti-DNA Fab A52 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4m61
TitleCrystal structure of unliganded anti-DNA Fab A52
Components
  • Fab A52 heavy chain
  • Fab A52 light chain
KeywordsIMMUNE SYSTEM / immunoglobulin fold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsStanfield, R.L. / Eilat, D. / Wilson, I.A.
CitationJournal: Proteins / Year: 2014
Title: Crystal structure determination of anti-DNA Fab A52.
Authors: Stanfield, R.L. / Eilat, D.
History
DepositionAug 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Aug 6, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fab A52 light chain
B: Fab A52 heavy chain
C: Fab A52 light chain
D: Fab A52 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,14723
Polymers95,3224
Non-polymers1,82519
Water13,854769
1
A: Fab A52 light chain
B: Fab A52 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,62212
Polymers47,6612
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-94 kcal/mol
Surface area19830 Å2
MethodPISA
2
C: Fab A52 light chain
D: Fab A52 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,52511
Polymers47,6612
Non-polymers8659
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-157 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.784, 61.380, 121.223
Angle α, β, γ (deg.)90.00, 96.51, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody Fab A52 light chain


Mass: 24150.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: NZB/NZW F1
#2: Antibody Fab A52 heavy chain


Mass: 23510.209 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: NZB/NZW F1
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 769 / 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: 2.05 Å3/Da / Density % sol: 39.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1.4 M ammonium sulfate, 0.07 M sodium citrate, 2% PEG400, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 28, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.62→43 Å / Num. all: 94152 / Num. obs: 94152 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 28.7
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4662 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
EPMRphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MRF

1mrf


Resolution: 1.62→21.694 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 24.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2323 9434 10.02 %
Rwork0.1919 --
obs0.1959 94118 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.62→21.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6690 0 95 769 7554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087114
X-RAY DIFFRACTIONf_angle_d1.1829725
X-RAY DIFFRACTIONf_dihedral_angle_d12.9182556
X-RAY DIFFRACTIONf_chiral_restr0.0841085
X-RAY DIFFRACTIONf_plane_restr0.0051218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.63840.3642970.35562781X-RAY DIFFRACTION95
1.6384-1.65770.3343130.28672877X-RAY DIFFRACTION97
1.6577-1.67790.31963300.25052796X-RAY DIFFRACTION97
1.6779-1.69910.3293130.25082837X-RAY DIFFRACTION96
1.6991-1.72150.29433370.25642782X-RAY DIFFRACTION97
1.7215-1.7450.27443270.23462800X-RAY DIFFRACTION96
1.745-1.770.29443320.23512779X-RAY DIFFRACTION96
1.77-1.79640.30813370.23832789X-RAY DIFFRACTION96
1.7964-1.82440.25513240.20972769X-RAY DIFFRACTION95
1.8244-1.85430.27292830.21442837X-RAY DIFFRACTION96
1.8543-1.88630.24923190.20682763X-RAY DIFFRACTION94
1.8863-1.92060.24742910.20582793X-RAY DIFFRACTION96
1.9206-1.95750.25893210.19342725X-RAY DIFFRACTION94
1.9575-1.99740.24272840.19782793X-RAY DIFFRACTION95
1.9974-2.04080.2332990.1932780X-RAY DIFFRACTION94
2.0408-2.08820.24523030.21072741X-RAY DIFFRACTION94
2.0882-2.14040.25023300.20412726X-RAY DIFFRACTION94
2.1404-2.19820.23873090.1882791X-RAY DIFFRACTION94
2.1982-2.26280.23023100.19152765X-RAY DIFFRACTION95
2.2628-2.33580.22632970.19082773X-RAY DIFFRACTION94
2.3358-2.41920.24493190.20292763X-RAY DIFFRACTION95
2.4192-2.51590.26523010.19582866X-RAY DIFFRACTION96
2.5159-2.63020.24913280.18942800X-RAY DIFFRACTION96
2.6302-2.76860.23023180.1922868X-RAY DIFFRACTION97
2.7686-2.94170.24373440.1982864X-RAY DIFFRACTION98
2.9417-3.16820.21653090.1912878X-RAY DIFFRACTION98
3.1682-3.48590.21563150.17212940X-RAY DIFFRACTION98
3.4859-3.98750.20793180.16452943X-RAY DIFFRACTION99
3.9875-5.01360.16773110.1453001X-RAY DIFFRACTION100
5.0136-21.69590.1963150.19153064X-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