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- PDB-5ihu: Crystal structure of bovine Fab B11 -

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Basic information

Entry
Database: PDB / ID: 5ihu
TitleCrystal structure of bovine Fab B11
Components
  • bovine Fab B11 heavy chain
  • bovine Fab B11 light chain
KeywordsIMMUNE SYSTEM / antibody fab ultralong CDRH3
Function / homology
Function and homology information


: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsStanfield, R. / Wilson, I.
CitationJournal: Sci Immunol / Year: 2016
Title: Conservation and diversity in the ultralong third heavy-chain complementarity-determining region of bovine antibodies.
Authors: Stanfield, R.L. / Wilson, I.A. / Smider, V.V.
History
DepositionFeb 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: bovine Fab B11 light chain
H: bovine Fab B11 heavy chain


Theoretical massNumber of molelcules
Total (without water)51,1402
Polymers51,1402
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-30 kcal/mol
Surface area22340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.410, 71.460, 88.320
Angle α, β, γ (deg.)90.00, 97.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody bovine Fab B11 light chain


Mass: 22548.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: Q3T101*PLUS
#2: Antibody bovine Fab B11 heavy chain


Mass: 28591.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 5% PEG 3000 30% PEG 400 10% glycerol 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.06→38.9 Å / Num. obs: 28518 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 45.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.8
Reflection shellResolution: 2.06→2.13 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.6 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K3D

4k3d


Resolution: 2.06→38.89 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.67
RfactorNum. reflection% reflection
Rfree0.2347 2372 8.32 %
Rwork0.1941 --
obs0.1975 28505 94.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 73.3 Å2
Refinement stepCycle: LAST / Resolution: 2.06→38.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 0 55 3611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033648
X-RAY DIFFRACTIONf_angle_d0.854964
X-RAY DIFFRACTIONf_dihedral_angle_d12.991279
X-RAY DIFFRACTIONf_chiral_restr0.03580
X-RAY DIFFRACTIONf_plane_restr0.003632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0603-2.10230.43041380.42571462X-RAY DIFFRACTION91
2.1023-2.14810.31251420.30751561X-RAY DIFFRACTION99
2.1481-2.1980.31931400.27311598X-RAY DIFFRACTION99
2.198-2.2530.32021150.30731366X-RAY DIFFRACTION92
2.253-2.31390.2565960.26391024X-RAY DIFFRACTION84
2.3139-2.3820.3081470.25481585X-RAY DIFFRACTION99
2.382-2.45880.32291490.24591586X-RAY DIFFRACTION98
2.4588-2.54670.35671400.26171541X-RAY DIFFRACTION96
2.5467-2.64870.29921410.2511567X-RAY DIFFRACTION97
2.6487-2.76920.24811490.23511601X-RAY DIFFRACTION99
2.7692-2.91510.27551460.22221603X-RAY DIFFRACTION99
2.9151-3.09770.27121420.21911595X-RAY DIFFRACTION99
3.0977-3.33670.22921480.20351611X-RAY DIFFRACTION99
3.3367-3.67230.2681390.18781576X-RAY DIFFRACTION97
3.6723-4.20320.21461430.16731603X-RAY DIFFRACTION97
4.2032-5.29340.15061500.13741624X-RAY DIFFRACTION99
5.2934-38.89720.21321470.16271630X-RAY DIFFRACTION98
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)
12.8143-0.34070.19528.71560.07665.794-0.1956-0.3566-0.55160.82210.08270.53540.3176-0.35550.10130.46520.05470.06880.56710.1040.57812.1383-38.92731.4928
23.91040.15472.52030.3741.01154.65910.2069-0.4728-0.2142-0.0654-0.139-0.25870.3269-0.6803-0.1240.3815-0.05560.0360.37010.01790.482-15.1501-40.63482.3064
33.40390.78310.50959.44470.51476.01620.1780.1036-0.22840.244-0.3361-1.04390.12640.21790.19090.2513-0.0062-0.0080.25910.0270.5509-12.4909-42.0543-4.4291
43.49050.1772.7236.084-0.57485.6829-0.0794-0.43680.08430.87460.12980.3284-0.597-0.411-0.02550.47320.09540.0730.52-0.02120.2717-0.2587-17.372826.5458
55.175-3.39662.49235.0277-3.08986.5682-0.9447-0.21631.07351.0487-0.09830.1014-1.70870.25741.05731.58580.0194-0.2330.91180.04620.994621.0648-33.300658.5048
63.89811.51722.80052.00761.73084.91720.0981-0.0822-0.09390.16560.03870.28870.5685-0.0321-0.09180.35650.08850.10340.2530.02370.3949-12.8294-28.79679.8775
77.3379-0.2298-0.45366.4790.55614.6031-0.2366-0.2443-0.51350.4039-0.06530.78470.4058-0.1520.24470.347-0.00650.04160.27270.08640.367-21.282-29.21565.337
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 3 through 102 )
2X-RAY DIFFRACTION2chain 'L' and (resid 103 through 128 )
3X-RAY DIFFRACTION3chain 'L' and (resid 129 through 211 )
4X-RAY DIFFRACTION4chain 'H' and (resid 1 through 100 )
5X-RAY DIFFRACTION5chain 'H' and (resid 101 through 149 )
6X-RAY DIFFRACTION6chain 'H' and (resid 150 through 200 )
7X-RAY DIFFRACTION7chain 'H' and (resid 201 through 270 )

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