[English] 日本語
Yorodumi
- PDB-4odw: Unliganded Fab structure of lipid A-specific antibody A6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4odw
TitleUnliganded Fab structure of lipid A-specific antibody A6
Components
  • A6 Fab (IgG2b kappa) light chain
  • A6 Fab (IgG2b) heavy chain
KeywordsIMMUNE SYSTEM / Carbohydrate binding
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.72 Å
AuthorsHaji-Ghassemi, O. / Evans, S.V.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for Antibody Recognition of Lipid A: INSIGHTS TO POLYSPECIFICITY TOWARD SINGLE-STRANDED DNA.
Authors: Haji-Ghassemi, O. / Muller-Loennies, S. / Rodriguez, T. / Brade, L. / Kosma, P. / Brade, H. / Evans, S.V.
History
DepositionJan 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Oct 7, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: A6 Fab (IgG2b kappa) light chain
H: A6 Fab (IgG2b) heavy chain
B: A6 Fab (IgG2b kappa) light chain
A: A6 Fab (IgG2b) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4105
Polymers95,2884
Non-polymers1221
Water28816
1
L: A6 Fab (IgG2b kappa) light chain
H: A6 Fab (IgG2b) heavy chain


Theoretical massNumber of molelcules
Total (without water)47,6442
Polymers47,6442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-25 kcal/mol
Surface area19390 Å2
MethodPISA
2
B: A6 Fab (IgG2b kappa) light chain
A: A6 Fab (IgG2b) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7663
Polymers47,6442
Non-polymers1221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-20 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.129, 69.235, 69.066
Angle α, β, γ (deg.)70.990, 72.390, 88.290
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21B
12H
22A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010L1 - 214
2010B1 - 214
1020H2 - 219
2020A2 - 219

NCS ensembles :
ID
1
2

-
Components

#1: Antibody A6 Fab (IgG2b kappa) light chain


Mass: 23851.348 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c
#2: Antibody A6 Fab (IgG2b) heavy chain


Mass: 23792.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 1.9 Å3/Da / Density % sol: 35.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, 35% (w/v) PEG 1000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 23, 2011 / Details: Vertical focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.7→65.27 Å / Num. all: 36601 / Num. obs: 18489 / % possible obs: 98.1 % / Redundancy: 2 % / Rmerge(I) obs: 0.04 / Χ2: 0.842 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.820.47218920.976198.3
2.8-2.9120.32118270.954198.2
2.91-3.0420.21418610.958198.4
3.04-3.220.1318600.918198.8
3.2-3.420.08818490.952198.5
3.4-3.6620.05418560.88198.6
3.66-4.0320.0418530.877197.9
4.03-4.6120.02518350.672197.7
4.61-5.8120.02418280.544197.5
5.81-3520.03118280.675197.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.72 Å33.9 Å
Translation2.72 Å33.9 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
MacromolecularCrystallography Data Collector software (MxDC)data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ODV

4odv


Resolution: 2.72→65.27 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.891 / WRfactor Rfree: 0.2528 / WRfactor Rwork: 0.2276 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8051 / SU B: 40.862 / SU ML: 0.364 / SU R Cruickshank DPI: 0.4541 / SU Rfree: 0.4822 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.482 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2566 833 5.1 %RANDOM
Rwork0.2313 ---
obs0.2325 16440 86.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.39 Å2 / Biso mean: 53.3046 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å21.13 Å20.96 Å2
2--4.59 Å20.69 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 2.72→65.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6534 0 8 16 6558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.026691
X-RAY DIFFRACTIONr_bond_other_d0.0020.026128
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.9579106
X-RAY DIFFRACTIONr_angle_other_deg2.149314181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8635843
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09423.876258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.648151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0831530
X-RAY DIFFRACTIONr_chiral_restr0.0850.21046
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217498
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021492
X-RAY DIFFRACTIONr_mcbond_it0.3641.3043394
X-RAY DIFFRACTIONr_mcbond_other0.3641.3033392
X-RAY DIFFRACTIONr_mcangle_it0.5841.9544229
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11L108760.18
12B108760.18
21H108580.13
22A108580.13
LS refinement shellResolution: 2.716→2.786 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 30 -
Rwork0.318 496 -
all-526 -
obs--36.83 %
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)
14.1057-1.1719-5.54022.55311.9947.9061-0.21810.2749-0.2420.1722-0.06170.33040.7832-0.42780.27980.6253-0.0952-0.1260.03710.04380.3803-8.7539-17.1494-4.9234
21.8359-0.5172-2.17693.28791.96657.40330.2933-0.01270.28970.2308-0.22330.02040.05210.032-0.070.1049-0.02280.01440.02230.02550.369-2.812-0.308-4.8967
30.9677-0.299-0.64161.92470.83378.6252-0.08160.25040.2323-0.18980.04290.0512-0.8598-0.2650.03870.3394-0.024-0.05170.07570.08140.5345-38.065742.836619.6875
41.5814-0.0806-0.77691.5822-0.50318.4442-0.09590.14130.1354-0.39040.01440.11080.06910.07460.08150.1149-0.0158-0.03510.01650.03250.3734-33.060128.757329.6754
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 214
2X-RAY DIFFRACTION2H2 - 221
3X-RAY DIFFRACTION3B1 - 214
4X-RAY DIFFRACTION4A2 - 219

+
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