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- PDB-5mhe: Crystal structure of anti-T4 Fab fragment with T4 -

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Basic information

Entry
Database: PDB / ID: 5mhe
TitleCrystal structure of anti-T4 Fab fragment with T4
Components(Fab-fragment) x 2
KeywordsIMMUNE SYSTEM / Fab-fragment / Ig fold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 3,5,3',5'-TETRAIODO-L-THYRONINE
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsParkkinen, T. / Rouvinen, J.
CitationJournal: To Be Published
Title: Crystal structures of anti-T4 Fab fragment
Authors: Parkkinen, T. / Rouvinen, J.
History
DepositionNov 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab-fragment
H: Fab-fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7486
Polymers48,6912
Non-polymers1,0574
Water6,035335
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-37 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.730, 55.330, 61.160
Angle α, β, γ (deg.)90.00, 97.77, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-497-

HOH

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody Fab-fragment


Mass: 23323.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): RV308
#2: Antibody Fab-fragment


Mass: 25367.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): RV308

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Non-polymers , 4 types, 339 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-T44 / 3,5,3',5'-TETRAIODO-L-THYRONINE


Mass: 776.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11I4NO4 / Comment: hormone*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.27 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.1 M ammonium sulphate, 25% PEG 3350, 0.1 M Hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 63198 / % possible obs: 93.6 % / Redundancy: 1.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.119 / Net I/σ(I): 7.66
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 0.65 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 1.49 / CC1/2: 0.6 / Rrim(I) all: 1.05 / % possible all: 91.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DQD

1dqd


Resolution: 1.9→19.835 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.98
RfactorNum. reflection% reflection
Rfree0.2265 1707 4.99 %
Rwork0.1783 --
obs0.1808 34191 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 41 335 3670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013420
X-RAY DIFFRACTIONf_angle_d1.0914658
X-RAY DIFFRACTIONf_dihedral_angle_d12.5012038
X-RAY DIFFRACTIONf_chiral_restr0.061518
X-RAY DIFFRACTIONf_plane_restr0.007586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95580.34561420.27932693X-RAY DIFFRACTION98
1.9558-2.01890.31781380.2582664X-RAY DIFFRACTION99
2.0189-2.0910.33181420.23962686X-RAY DIFFRACTION99
2.091-2.17460.25521410.21072681X-RAY DIFFRACTION99
2.1746-2.27350.24041410.19932695X-RAY DIFFRACTION99
2.2735-2.39310.24451410.19512696X-RAY DIFFRACTION99
2.3931-2.54280.27211420.19912702X-RAY DIFFRACTION99
2.5428-2.73860.24821440.1892725X-RAY DIFFRACTION99
2.7386-3.01340.23231430.17752716X-RAY DIFFRACTION100
3.0134-3.44750.21091430.16492733X-RAY DIFFRACTION99
3.4475-4.3360.1941450.14142740X-RAY DIFFRACTION99
4.336-19.83630.17281450.15292753X-RAY DIFFRACTION98

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