[English] 日本語
Yorodumi
- PDB-9i6q: Structure of Fab-Fragment GB11 agains tumour associated carbohydr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9i6q
TitleStructure of Fab-Fragment GB11 agains tumour associated carbohydrate antigens.
Components
  • Fab fragment variable chain
  • Heavy chain
KeywordsIMMUNE SYSTEM / Antibody / FAB fragment / apo
Function / homologyDI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsFreitag, A. / Khilji, S.K. / Nedielkov, R. / Kumar, S.M. / Krummhaar, M. / Luehle, J. / Goerdeler, F. / Arndt, J. / Kamphues, C. / Mroginski, M.A. ...Freitag, A. / Khilji, S.K. / Nedielkov, R. / Kumar, S.M. / Krummhaar, M. / Luehle, J. / Goerdeler, F. / Arndt, J. / Kamphues, C. / Mroginski, M.A. / Roth, C. / Seeberger, P.H. / Moeller, H.M. / Moscovitz, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Jacs Au / Year: 2026
Title: Integrative Approach to Develop and Characterize Antibodies against the Cancer-Associated Antigen Sialyl Lewis A (CA 19-9).
Authors: Freitag, A. / Khilji, S.K. / Nedielkov, R. / M Kumar, S. / Krummhaar, M. / Arndt, J. / Moreira, G.M.S.G. / Luhle, J. / Goerdeler, F. / Kamphues, C. / Mroginski, M.A. / Roth, C. / Seeberger, ...Authors: Freitag, A. / Khilji, S.K. / Nedielkov, R. / M Kumar, S. / Krummhaar, M. / Arndt, J. / Moreira, G.M.S.G. / Luhle, J. / Goerdeler, F. / Kamphues, C. / Mroginski, M.A. / Roth, C. / Seeberger, P.H. / Moller, H.M. / Moscovitz, O.
History
DepositionJan 31, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.1May 13, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Heavy chain
L: Fab fragment variable chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,78623
Polymers53,5142
Non-polymers2,27321
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.160, 109.160, 40.268
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11H-521-

HOH

-
Components

#1: Antibody Heavy chain


Mass: 29539.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: spleen
#2: Antibody Fab fragment variable chain


Mass: 23974.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: spleen
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: DL-Malic acid, Citric acid, PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.86→54.58 Å / Num. obs: 40412 / % possible obs: 100 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.086 / Rrim(I) all: 0.211 / Net I/σ(I): 7.7
Reflection shellResolution: 1.86→1.9 Å / Redundancy: 11.2 % / Rmerge(I) obs: 2.721 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2462 / CC1/2: 0.376 / Rpim(I) all: 0.847 / Rrim(I) all: 2.852 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→48.866 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.622 / SU ML: 0.137 / Cross valid method: FREE R-VALUE / ESU R: 0.148 / ESU R Free: 0.139
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2387 1959 4.851 %
Rwork0.2004 38423 -
all0.202 --
obs-40382 99.928 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.946 Å2
Baniso -1Baniso -2Baniso -3
1-0.988 Å2-0 Å2-0 Å2
2--0.988 Å2-0 Å2
3----1.976 Å2
Refinement stepCycle: LAST / Resolution: 1.86→48.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 138 202 3646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123521
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163230
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.6474712
X-RAY DIFFRACTIONr_angle_other_deg0.6431.5627486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3975427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.84516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.09810543
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.4610139
X-RAY DIFFRACTIONr_chiral_restr0.0830.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023946
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02774
X-RAY DIFFRACTIONr_nbd_refined0.1940.2566
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.23012
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21665
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21920
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2189
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0290.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1320.29
X-RAY DIFFRACTIONr_nbd_other0.1270.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.224
X-RAY DIFFRACTIONr_mcbond_it2.2131.9731714
X-RAY DIFFRACTIONr_mcbond_other2.211.9731714
X-RAY DIFFRACTIONr_mcangle_it3.3013.5282139
X-RAY DIFFRACTIONr_mcangle_other3.3023.532140
X-RAY DIFFRACTIONr_scbond_it3.6112.4951807
X-RAY DIFFRACTIONr_scbond_other3.612.4971808
X-RAY DIFFRACTIONr_scangle_it5.0014.232573
X-RAY DIFFRACTIONr_scangle_other5.0014.2312574
X-RAY DIFFRACTIONr_lrange_it7.4821.8183735
X-RAY DIFFRACTIONr_lrange_other7.4821.8243736
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.86-1.9080.3561370.33128400.33229790.9070.91999.93290.323
1.908-1.9610.3371240.32127340.32228620.9190.92899.86020.306
1.961-2.0170.3021180.29827060.29828260.9420.93799.92920.285
2.017-2.0790.2941480.26825420.26926920.9280.94199.92570.25
2.079-2.1470.3011360.23825280.24126650.9340.96499.96250.22
2.147-2.2230.2731130.21924260.22125410.9550.97199.92130.194
2.223-2.3060.2561130.22923430.2324580.9610.96899.91860.204
2.306-2.40.2981250.2222650.22423910.9460.97199.95820.192
2.4-2.5070.2841070.21521870.21822940.9540.9741000.19
2.507-2.6290.261870.21120900.21321770.9550.9751000.185
2.629-2.7710.2691050.19519860.19920920.9530.97899.95220.172
2.771-2.9380.261010.20118600.20419610.9550.9751000.18
2.938-3.140.243840.1917990.19318830.9610.9791000.176
3.14-3.3910.209980.18616370.18717360.9690.98199.94240.179
3.391-3.7120.222690.17415240.17615940.9590.98399.93730.174
3.712-4.1480.229960.16313630.16714590.9650.9851000.167
4.148-4.7830.147620.13412310.13412930.9860.991000.142
4.783-5.8450.171660.14110460.14311130.9830.9999.91010.15
5.845-8.2070.188440.188280.188720.9760.9831000.185
8.207-48.8660.251260.2234880.2245200.9570.96498.84620.276
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)
10.58690.10520.05642.2956-0.37160.750.0290.0196-0.1058-0.01260.02280.04690.19-0.0405-0.05180.0558-0.00820.00010.0041-0.00160.146245.525216.88469.6818
20.4721-0.84840.31551.9048-0.26280.47160.0535-0.0758-0.26460.09610.03230.50770.2012-0.142-0.08580.1456-0.05210.02810.0723-0.00290.397728.187414.593912.9196
Refinement TLS groupSelection: ALL

+
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