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- PDB-4krn: Nanobody/VHH domain EgA1 -

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Basic information

Entry
Database: PDB / ID: 4krn
TitleNanobody/VHH domain EgA1
ComponentsNanobody/VHH domain EgA1
KeywordsIMMUNE SYSTEM / nanobody / VHH domain / Camelid VH domain / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.553 Å
AuthorsFerguson, K.M. / Schmitz, K.R.
CitationJournal: Structure / Year: 2013
Title: Structural Evaluation of EGFR Inhibition Mechanisms for Nanobodies/VHH Domains.
Authors: Schmitz, K.R. / Bagchi, A. / Roovers, R.C. / van Bergen En Henegouwen, P.M. / Ferguson, K.M.
History
DepositionMay 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 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
A: Nanobody/VHH domain EgA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6422
Polymers15,5461
Non-polymers961
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.769, 52.769, 62.724
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Antibody Nanobody/VHH domain EgA1


Mass: 15546.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pET22b / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 3.03 Å3/Da / Density % sol: 59.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG3350, 0.2 M ammonium sulfate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2008
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.55→31.357 Å / Num. all: 24694 / Num. obs: 24694 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.037 / Χ2: 1.705 / Net I/σ(I): 19
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.55-1.613.50.28323151.222194.5
1.61-1.674.10.23724631.296199.8
1.67-1.754.40.17624721.353199.9
1.75-1.844.50.12824731.4271100
1.84-1.954.50.08824981.706199.9
1.95-2.14.50.06924842.047199.8
2.1-2.324.50.05224821.932199.9
2.32-2.654.50.04324901.8651100
2.65-3.344.50.03725042.429199.9
3.34-504.40.02525131.539198.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
JBluIce-EPICSdata collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I3V

1i3v


Resolution: 1.553→26.96 Å / Cor.coef. Fo:Fc: 0.9571 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.2422 / WRfactor Rwork: 0.2094 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8697 / SU B: 2.404 / SU ML: 0.042 / SU R Cruickshank DPI: 0.0875 / SU Rfree: 0.0768 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 1253 5.1 %RANDOM
Rwork0.1987 ---
obs0.2004 23401 99.2 %-
all-24651 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.16 Å2 / Biso mean: 21.8934 Å2 / Biso min: 13.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.553→26.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms968 0 5 84 1057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221021
X-RAY DIFFRACTIONr_angle_refined_deg1.1111.9441398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0595134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.7222.04544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15515144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.875159
X-RAY DIFFRACTIONr_chiral_restr0.0730.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02798
X-RAY DIFFRACTIONr_nbd_refined0.1930.2388
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2697
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.263
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.27
X-RAY DIFFRACTIONr_mcbond_it0.8221.5649
X-RAY DIFFRACTIONr_mcangle_it1.36521011
X-RAY DIFFRACTIONr_scbond_it1.993447
X-RAY DIFFRACTIONr_scangle_it2.6144.5382
LS refinement shellResolution: 1.553→1.593 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 85 -
Rwork0.258 1586 -
all-1671 -
obs--93.09 %

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