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- PDB-6z7x: Insulin analytical antibody OXI-005 Fab -

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Basic information

Entry
Database: PDB / ID: 6z7x
TitleInsulin analytical antibody OXI-005 Fab
Components
  • OXI-005 Fab Heavy chain
  • OXI-005 Fab Light chain
KeywordsPROTEIN BINDING / insulin / analytical antibody / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsJohansson, E.
CitationJournal: Protein Sci. / Year: 2021
Title: Insulin binding to the analytical antibody sandwich pair OXI-005 and HUI-018: Epitope mapping and binding properties.
Authors: Johansson, E. / Wu, X. / Yu, B. / Yang, Z. / Cao, Z. / Wiberg, C. / Jeppesen, C.B. / Poulsen, F.
History
DepositionJun 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OXI-005 Fab Light chain
B: OXI-005 Fab Heavy chain


Theoretical massNumber of molelcules
Total (without water)47,2972
Polymers47,2972
Non-polymers00
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-28 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.190, 94.140, 52.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-357-

HOH

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Components

#1: Antibody OXI-005 Fab Light chain


Mass: 23539.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody OXI-005 Fab Heavy chain


Mass: 23757.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium sulfate, 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→45.92 Å / Num. obs: 23390 / % possible obs: 99.88 % / Redundancy: 6.4 % / Biso Wilson estimate: 43.81 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.08822 / Rpim(I) all: 0.03762 / Rrim(I) all: 0.09612 / Net I/σ(I): 12.75
Reflection shellResolution: 2.15→2.227 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.127 / Mean I/σ(I) obs: 1.54 / Num. unique obs: 14881 / CC1/2: 0.612 / CC star: 0.871 / Rpim(I) all: 0.4737 / Rrim(I) all: 1.224 / % possible all: 99.91

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Processing

Software
NameVersionClassification
PHENIXdev_3714refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XKN

2xkn


Resolution: 2.15→45.92 Å / SU ML: 0.3321 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 28.2289
RfactorNum. reflection% reflection
Rfree0.2529 2182 4.98 %
Rwork0.1951 --
obs0.198 23389 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.6 Å2
Refinement stepCycle: LAST / Resolution: 2.15→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 0 186 3506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00863409
X-RAY DIFFRACTIONf_angle_d1.01774644
X-RAY DIFFRACTIONf_chiral_restr0.0556520
X-RAY DIFFRACTIONf_plane_restr0.006593
X-RAY DIFFRACTIONf_dihedral_angle_d21.44421225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.30551380.30472630X-RAY DIFFRACTION99.86
2.2-2.250.41921370.30012595X-RAY DIFFRACTION99.96
2.25-2.30.30331360.28512558X-RAY DIFFRACTION99.74
2.3-2.370.35271360.28772604X-RAY DIFFRACTION99.6
2.37-2.440.35521330.2752576X-RAY DIFFRACTION98.44
2.44-2.510.29621370.2622616X-RAY DIFFRACTION99.82
2.51-2.60.39061350.2592613X-RAY DIFFRACTION100
2.6-2.710.38071330.25072588X-RAY DIFFRACTION99.96
2.71-2.830.26441420.22322636X-RAY DIFFRACTION99.93
2.83-2.980.29951350.21412560X-RAY DIFFRACTION99.85
2.98-3.170.27431330.20582639X-RAY DIFFRACTION99.89
3.17-3.410.27281380.20162577X-RAY DIFFRACTION99.09
3.41-3.760.2391370.1812613X-RAY DIFFRACTION99.64
3.76-4.30.22891390.16282614X-RAY DIFFRACTION99.85
4.3-5.410.18561340.13892589X-RAY DIFFRACTION99.82
5.42-45.920.19411390.16372589X-RAY DIFFRACTION99.13

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