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- PDB-8gv1: Crystal structure of anti-FX IgG fab with FAST-Ig mutations -

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Basic information

Entry
Database: PDB / ID: 8gv1
TitleCrystal structure of anti-FX IgG fab with FAST-Ig mutations
Components
  • Anti-factor X IgG fab heavy chain
  • Anti-factor X IgG fab light chain
KeywordsIMMUNE SYSTEM / BISPECIFIC ANTIBODY / FAST-IG / NXT007 / HEMOPHILIA A / FACTOR X
Function / homologyACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.186 Å
AuthorsKoga, H. / Yamano, T. / Fukami, T.A. / Sampei, Z. / Shiraiwa, H. / Torizawa, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mabs / Year: 2023
Title: Efficient production of bispecific antibody by FAST-Ig TM and its application to NXT007 for the treatment of hemophilia A.
Authors: Koga, H. / Yamano, T. / Betancur, J. / Nagatomo, S. / Ikeda, Y. / Yamaguchi, K. / Nabuchi, Y. / Sato, K. / Teranishi-Ikawa, Y. / Sato, M. / Hirayama, H. / Hayasaka, A. / Torizawa, T. / ...Authors: Koga, H. / Yamano, T. / Betancur, J. / Nagatomo, S. / Ikeda, Y. / Yamaguchi, K. / Nabuchi, Y. / Sato, K. / Teranishi-Ikawa, Y. / Sato, M. / Hirayama, H. / Hayasaka, A. / Torizawa, T. / Haraya, K. / Sampei, Z. / Shiraiwa, H. / Kitazawa, T. / Igawa, T. / Kuramochi, T.
History
DepositionSep 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-factor X IgG fab heavy chain
B: Anti-factor X IgG fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,76731
Polymers46,9732
Non-polymers1,79429
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint26 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.89, 62.298, 81.636
Angle α, β, γ (deg.)90, 105.55, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Anti-factor X IgG fab heavy chain


Mass: 24236.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Anti-factor X IgG fab light chain


Mass: 22736.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium acetate trihydrate [NaAcet], 20.0 %w/v Polyethylene glycol 3350 [PEG 3350]

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.186→49.558 Å / Num. obs: 104460 / % possible obs: 93.5 % / Redundancy: 4.74 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.999 / CC1/2 anomalous: -0.117 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.0183 / Rrim(I) all: 0.0406 / AbsDiff over sigma anomalous: 0.615 / Baniso tensor eigenvalue 1: 15 Å2 / Baniso tensor eigenvalue 2: 17.8 Å2 / Baniso tensor eigenvalue 3: 16.8 Å2 / Baniso tensor eigenvector 1 ortho1: 0.9528 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0.3035 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: -0.3035 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 0.9528 / Aniso diffraction limit 1: 1.186 Å / Aniso diffraction limit 2: 1.3 Å / Aniso diffraction limit 3: 1.293 Å / Aniso diffraction limit axis 1 ortho1: 0.85358 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0.52105 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: -0.52105 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 0.85358 / Net I/σ(I): 11.42 / Num. measured all: 495020 / Orthogonalization convention: pdb / % possible anomalous: 91.3 / % possible ellipsoidal: 93.5 / % possible ellipsoidal anomalous: 91.3 / % possible spherical: 78.8 / % possible spherical anomalous: 76.8 / Redundancy anomalous: 2.44
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
3.508-49.5584.550.02528.892378423784522352230.999-0.1260.01280.02820.41698.199.498.199.498.12.3999.4
2.778-3.5084.630.026827.732415424154522252220.999-0.110.01350.03010.46197.699.797.699.797.62.3999.7
2.425-2.7784.840.030625.882528525285522452240.999-0.0760.01520.03430.5299.299.999.299.999.22.4799.9
2.202-2.4254.510.034823.082354523545522352230.998-0.0370.01810.03940.56897.199.897.199.897.12.3399.8
2.042-2.2024.410.038821.262302723027522152210.998-0.0020.02030.0440.59795.899.895.899.895.82.399.8
1.922-2.0424.650.046519.182429024290522452240.997-0.0140.02380.05240.61496.899.796.899.796.82.4199.7
1.825-1.9224.810.059416.482509825098522352230.997-0.0070.02970.06660.63297.699.997.699.997.62.4799.9
1.744-1.8254.860.07613.562539825398522352230.995-0.0170.03780.08520.65698.299.898.299.898.22.4999.8
1.677-1.7444.880.103110.652548025480522452240.991-0.0260.05150.11570.66398.799.998.799.998.72.4999.9
1.619-1.6774.50.13158.372347523475522252220.984-0.0180.06870.1490.6729710097100972.33100
1.568-1.6194.670.16437.052440924409522452240.978-0.020.08410.18530.66297.599.897.599.897.52.499.8
1.523-1.5684.40.20415.562298422984522352230.966-0.0250.10770.23170.6495.299.895.299.895.22.399.8
1.483-1.5234.650.25754.642429324293522252220.9490.0150.13120.29020.6696.599.896.599.896.52.4199.8
1.446-1.4834.710.33743.622458924589522352230.9200.17050.37950.6449710097100972.43100
1.413-1.4464.710.4053.042459724597522352230.8760.0170.20550.45610.65396.499.496.499.496.42.4399.4
1.381-1.4134.90.52.552559725597522452240.8340.0010.24960.56080.64692.594.492.594.492.52.5194.4
1.35-1.3814.870.60562.112539825398521952190.791-0.0090.30340.67930.64288.590.488.590.488.52.4990.4
1.322-1.354.780.70591.792499124991522552250.7190.0050.35780.79370.65185.286.885.286.885.22.4586.8
1.289-1.3224.950.8521.532583625836522252220.645-0.0110.42430.9540.64971.97371.970.769.72.5273
1.186-1.2895.510.96681.442879028790522652260.610.0110.45191.06880.64757.157.257.117.817.62.857.2

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Processing

Software
NameVersionClassification
autoPROCdata processing
Aimless0.7.7data scaling
STARANISO2.3.63data scaling
PHENIX1.20.1refinement
XDSJan 31, 2020data reduction
PHASERphasing
BUSTER2.11.8 (3-FEB-2022)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DK3

5dk3


Resolution: 1.186→49.56 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / SU R Cruickshank DPI: 0.055 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.057 / SU Rfree Blow DPI: 0.058 / SU Rfree Cruickshank DPI: 0.056
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 5168 -RANDOM
Rwork0.2059 ---
obs0.2069 104460 78.8 %-
Displacement parametersBiso mean: 28.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.1801 Å20 Å2-0.1325 Å2
2--0.14 Å20 Å2
3---0.0401 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.186→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3167 0 116 467 3750
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083430HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.044653HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1141SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes582HARMONIC5
X-RAY DIFFRACTIONt_it3430HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion461SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3387SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.37
X-RAY DIFFRACTIONt_other_torsion16.31
LS refinement shellResolution: 1.19→1.26 Å
RfactorNum. reflection% reflection
Rfree0.3134 86 -
Rwork0.2919 --
obs0.2928 2090 9.63 %

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