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- PDB-3e8u: Crystal structure and thermodynamic analysis of diagnostic Fab 10... -

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Basic information

Entry
Database: PDB / ID: 3e8u
TitleCrystal structure and thermodynamic analysis of diagnostic Fab 106.3 complexed with BNP 5-13 (C10A) reveal basis of selective molecular recognition
Components
  • BNP peptide epitope
  • Fab 106.3 heavy chain
  • Fab 106.3 light chain
KeywordsIMMUNE SYSTEM / Fab 106.3 / IgG1 / Brain Natriuretic Peptide (BNP)
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsLongenecker, K.L. / Ruan, Q. / Fry, E.H. / Saldana, S.S. / Brophy, S.E. / Richardson, P.L. / Tetin, S.Y.
CitationJournal: Proteins / Year: 2009
Title: Crystal structure and thermodynamic analysis of diagnostic mAb 106.3 complexed with BNP 5-13 (C10A).
Authors: Longenecker, K.L. / Ruan, Q. / Fry, E.H. / Saldana, S.C. / Brophy, S.E. / Richardson, P.L. / Tetin, S.Y.
History
DepositionAug 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab 106.3 heavy chain
L: Fab 106.3 light chain
P: BNP peptide epitope


Theoretical massNumber of molelcules
Total (without water)48,1493
Polymers48,1493
Non-polymers00
Water7,656425
1
H: Fab 106.3 heavy chain
L: Fab 106.3 light chain
P: BNP peptide epitope

H: Fab 106.3 heavy chain
L: Fab 106.3 light chain
P: BNP peptide epitope


Theoretical massNumber of molelcules
Total (without water)96,2986
Polymers96,2986
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area12230 Å2
ΔGint-70 kcal/mol
Surface area36560 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-32 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.900, 88.878, 138.509
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody Fab 106.3 heavy chain


Mass: 23394.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
#2: Antibody Fab 106.3 light chain


Mass: 23761.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
#3: Protein/peptide BNP peptide epitope


Mass: 993.057 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 25672 / % possible obs: 90.3 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.089 / Χ2: 1.055
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.1820.35615081.10253.7
2.18-2.262.50.36220041.06371.7
2.26-2.373.30.34324501.0986.5
2.37-2.494.40.32526751.12595.7
2.49-2.655.50.27327331.06597.3
2.65-2.855.90.19727801.0898.4
2.85-3.1460.12728141.05198.9
3.14-3.596.30.07528281.04199.6
3.59-4.5270.04928851.019100
4.52-507.10.04129951.02799.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.1→44.73 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.209 / WRfactor Rwork: 0.163 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.835 / SU B: 5.039 / SU ML: 0.134 / SU R Cruickshank DPI: 0.263 / SU Rfree: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.263 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1314 5.1 %RANDOM
Rwork0.185 ---
obs0.188 25645 90.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 47.51 Å2 / Biso mean: 20.195 Å2 / Biso min: 5.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 0 425 3791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223456
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.9424711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5135435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45624.795146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82715534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3271511
X-RAY DIFFRACTIONr_chiral_restr0.0860.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022655
X-RAY DIFFRACTIONr_nbd_refined0.1840.21465
X-RAY DIFFRACTIONr_nbtor_refined0.2970.22282
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2380
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.220
X-RAY DIFFRACTIONr_mcbond_it0.5581.52234
X-RAY DIFFRACTIONr_mcangle_it0.98323541
X-RAY DIFFRACTIONr_scbond_it1.42931413
X-RAY DIFFRACTIONr_scangle_it2.2894.51170
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 65 -
Rwork0.238 1002 -
all-1067 -
obs--51.85 %

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