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- PDB-5yup: Crystal Structure of the Fab fragment of FVIIa antibody mAb4F5 -

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Basic information

Entry
Database: PDB / ID: 5yup
TitleCrystal Structure of the Fab fragment of FVIIa antibody mAb4F5
Components
  • the heavy chain of the Fab fragment of FVIIa antibody mAb4F5
  • the light chain of the Fab fragment of FVIIa antibody mAb4F5
KeywordsIMMUNE SYSTEM / FVIIa / antibodies / Fab4F5 / inhibition / coagulation / STRUCTURAL PROTEIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsJiang, L.G. / Persson, E. / Huang, M.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31400637 China
CitationJournal: Res Pract Thromb Haemost / Year: 2019
Title: Crystal structure, epitope, and functional impact of an antibody against a superactive FVIIa provide insights into allosteric mechanism.
Authors: Jiang, L.G. / Xie, X. / Li, J. / Persson, E. / Huang, M.D.
History
DepositionNov 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: the heavy chain of the Fab fragment of FVIIa antibody mAb4F5
L: the light chain of the Fab fragment of FVIIa antibody mAb4F5


Theoretical massNumber of molelcules
Total (without water)47,4242
Polymers47,4242
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-31 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.640, 141.640, 141.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Antibody the heavy chain of the Fab fragment of FVIIa antibody mAb4F5


Mass: 23593.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody the light chain of the Fab fragment of FVIIa antibody mAb4F5


Mass: 23830.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2.3M ammonium sulfate, 100mM Tris-HCl pH 7.4, 5% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.81→70.82 Å / Num. obs: 43048 / % possible obs: 100 % / Redundancy: 15 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 25.9
Reflection shellResolution: 1.81→1.84 Å / Rmerge(I) obs: 1.8 / Num. unique obs: 2259

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BRR AND 2R4R

2brr

2r4r


Resolution: 1.81→70.82 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 2067 4.8 %
Rwork0.207 --
obs0.209 43047 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→70.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3333 0 0 131 3464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093419
X-RAY DIFFRACTIONf_angle_d1.314650
X-RAY DIFFRACTIONf_dihedral_angle_d13.0951216
X-RAY DIFFRACTIONf_chiral_restr0.052523
X-RAY DIFFRACTIONf_plane_restr0.006596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8103-1.85240.30981240.26422743X-RAY DIFFRACTION100
1.8524-1.89870.31461330.25772709X-RAY DIFFRACTION100
1.8987-1.950.28051410.23642692X-RAY DIFFRACTION100
1.95-2.00740.27311330.23542747X-RAY DIFFRACTION100
2.0074-2.07220.24091340.22112698X-RAY DIFFRACTION100
2.0722-2.14630.26631570.22692683X-RAY DIFFRACTION100
2.1463-2.23220.261130.21162727X-RAY DIFFRACTION100
2.2322-2.33380.27461420.22992727X-RAY DIFFRACTION100
2.3338-2.45690.28571690.23272693X-RAY DIFFRACTION100
2.4569-2.61080.26821350.22672727X-RAY DIFFRACTION100
2.6108-2.81240.28531460.22562704X-RAY DIFFRACTION100
2.8124-3.09540.33231200.22142770X-RAY DIFFRACTION100
3.0954-3.54330.22151420.20492749X-RAY DIFFRACTION100
3.5433-4.46410.21261220.17882770X-RAY DIFFRACTION100
4.4641-70.87420.22591560.19062841X-RAY DIFFRACTION100

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