[English] 日本語
Yorodumi
- PDB-8xs2: Crystal structure of Fab fragment of anti-osteocalcin C-terminal ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xs2
TitleCrystal structure of Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219 with addition of fluorophore TAMRA
Components
  • Heavy chain fragment (Fd) of anti-osteocalcin antibody KTM219
  • Light chain of anti-osteocalcin antibody KTM219
KeywordsIMMUNE SYSTEM / Antibody / Immunoglobulin fold / Osteocalcin / Quenchbody (Q-body) / Open sandwich immunoassay
Function / homologyACETATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsYazaki, S. / Ueda, H. / Arai, R.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19H02522, JP17KK0104, JP16K05841, JP16H00761, JP24780097, JP15H04191, JP18H03851 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)Cooperative Research Program of Network Joint Research Center for Materials and Devices Japan
Citation
Journal: Int J Mol Sci / Year: 2025
Title: Crystal Structures of Antigen-Binding Fragment of Anti-Osteocalcin Antibody KTM219.
Authors: Yazaki, S. / Komatsu, M. / Dong, J. / Ueda, H. / Arai, R.
#1: Journal: Sci Rep / Year: 2014
Title: Ultra Q-bodies: quench-based antibody probes that utilize dye-dye interactions with enhanced antigen-dependent fluorescence.
Authors: Abe, R. / Jeong, H.J. / Arakawa, D. / Dong, J. / Ohashi, H. / Kaigome, R. / Saiki, F. / Yamane, K. / Takagi, H. / Ueda, H.
#2: Journal: Sensors (Basel) / Year: 2021
Title: Recent Advances in Quenchbody, a Fluorescent Immunosensor.
Authors: Dong, J. / Ueda, H.
History
DepositionJan 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: 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.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 fragment (Fd) of anti-osteocalcin antibody KTM219
L: Light chain of anti-osteocalcin antibody KTM219
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5814
Polymers51,4632
Non-polymers1182
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-23 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.185, 69.520, 96.653
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

-
Components

#1: Antibody Heavy chain fragment (Fd) of anti-osteocalcin antibody KTM219


Mass: 26202.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: HYBRIDOMA KTM-219 / Plasmid: pET-Fab(KTM219) / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 Express lysY
#2: Antibody Light chain of anti-osteocalcin antibody KTM219


Mass: 25259.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: HYBRIDOMA KTM-219 / Plasmid: pET-Fab(KTM219) / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 Express lysY
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.16 Å3/Da / Density % sol: 43.07 % / Description: Plate-like crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 0.3 M Ammonium Acetate, 25% PEG 3350, 0.6 mM TAMRA

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 23, 2019
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 24972 / % possible obs: 99.5 % / Redundancy: 12.6 % / Biso Wilson estimate: 27.6 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.033 / Rrim(I) all: 0.12 / Χ2: 0.993 / Net I/av σ(I): 23.6 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.14-2.1811.81.0152.4712160.8150.9480.3021.060.91898.1
2.18-2.2212.20.9212.812200.8670.9640.270.960.95799.9
2.22-2.2612.30.8393.2112170.8940.9720.2460.8750.94598.5
2.26-2.3112.30.7823.4312340.9080.9750.2290.8150.94999.6
2.31-2.3612.20.6574.3112120.9330.9830.1940.6850.95799.1
2.36-2.4111.80.6344.3112200.930.9820.190.6620.97298.9
2.41-2.4712.50.5415.4212450.9630.9910.1570.5640.98399.7
2.47-2.5412.20.4266.6712250.970.9920.1250.4440.98199.4
2.54-2.6113.30.3618.1812280.9790.9950.1020.3760.97199.3
2.61-2.713.20.3079.9112200.9850.9960.0870.320.99699.3
2.7-2.7913.10.2511.212440.9870.9970.0710.261.01999.5
2.79-2.913.10.20814.312610.9910.9980.0590.2161.04399.6
2.9-3.0412.70.16816.912300.9940.9980.0490.1751.06899.7
3.04-3.212.50.13120.712460.9960.9990.0380.1371.07399.8
3.2-3.412.90.10128.412610.9970.9990.0290.1051.11899.8
3.4-3.6613.50.07540.312640.99910.0210.0781.1399.8
3.66-4.0313.30.06344.812670.99910.0180.0651.077100
4.03-4.6112.30.04853.212700.99910.0140.051.041100
4.61-5.8112.80.04157.813040.99910.0120.0430.91399.9
5.81-50120.03358.91388110.010.0350.73699.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X5X

5x5x


Resolution: 2.14→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.033 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.275 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24426 1193 4.9 %RANDOM
Rwork0.20245 ---
obs0.20438 23209 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.028 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.64 Å2
Refinement stepCycle: 1 / Resolution: 2.14→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3237 0 8 257 3502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193327
X-RAY DIFFRACTIONr_bond_other_d0.0060.023039
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9474523
X-RAY DIFFRACTIONr_angle_other_deg0.90337054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0195427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08125.079126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21515531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.643156
X-RAY DIFFRACTIONr_chiral_restr0.0760.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213757
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02731
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.642.9341712
X-RAY DIFFRACTIONr_mcbond_other1.6372.931709
X-RAY DIFFRACTIONr_mcangle_it2.7114.3832134
X-RAY DIFFRACTIONr_mcangle_other2.7114.3852135
X-RAY DIFFRACTIONr_scbond_it1.7293.0341614
X-RAY DIFFRACTIONr_scbond_other1.7283.0351615
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8794.4712389
X-RAY DIFFRACTIONr_long_range_B_refined5.15123.4773685
X-RAY DIFFRACTIONr_long_range_B_other5.15723.4793685
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.143→2.199 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 63 -
Rwork0.276 1265 -
obs--72.37 %

+
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