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- PDB-4m43: Crystal structure of anti-rabies glycoprotein Fab 523-11 -

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Basic information

Entry
Database: PDB / ID: 4m43
TitleCrystal structure of anti-rabies glycoprotein Fab 523-11
Components
  • Fragment antigen-binding 523-11 heavy chain
  • Fragment antigen-binding 523-11 light chain
KeywordsIMMUNE SYSTEM / Immunoglobulin fold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsStanfield, R.L. / Wilson, I.A. / Wunner, W.H.
CitationJournal: To be Published
Title: Crystal structure of anti-rabies glycoprotein Fab 523-11
Authors: Stanfield, R.L. / Wilson, I.A. / Wunner, W.H.
History
DepositionAug 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Data collection / Derived calculations / Category: reflns_shell / struct_site
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all ..._reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 20, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fragment antigen-binding 523-11 light chain
H: Fragment antigen-binding 523-11 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5177
Polymers47,0442
Non-polymers4725
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-65 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.431, 123.147, 42.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a dimer of L and H chains contained within the asymmetric unit

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Components

#1: Antibody Fragment antigen-binding 523-11 light chain / FAB


Mass: 23346.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fragment antigen-binding 523-11 heavy chain / FAB


Mass: 23697.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.5M ammonium sulfate, 0.1M imidazole malate, 10% ethanol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 5, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→29.6 Å / Num. all: 39028 / Num. obs: 39028 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 16.4
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 4 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1965 / % possible all: 99.6

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Processing

Software
NameVersionClassification
EPMRphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IGI

1igi


Resolution: 1.85→29.598 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 23.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2322 2000 5.13 %
Rwork0.1941 --
obs0.196 38994 99.73 %
all-38994 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→29.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 0 27 138 3472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113430
X-RAY DIFFRACTIONf_angle_d1.3594666
X-RAY DIFFRACTIONf_dihedral_angle_d13.5611216
X-RAY DIFFRACTIONf_chiral_restr0.083524
X-RAY DIFFRACTIONf_plane_restr0.007587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89630.31891380.26412564X-RAY DIFFRACTION100
1.8963-1.94750.29291430.24232619X-RAY DIFFRACTION100
1.9475-2.00480.3041390.23252587X-RAY DIFFRACTION100
2.0048-2.06950.29771400.21232590X-RAY DIFFRACTION100
2.0695-2.14350.26321420.19772629X-RAY DIFFRACTION100
2.1435-2.22930.25841420.20022614X-RAY DIFFRACTION100
2.2293-2.33070.26221410.19762612X-RAY DIFFRACTION100
2.3307-2.45350.23391420.19772634X-RAY DIFFRACTION100
2.4535-2.60710.2471420.21042626X-RAY DIFFRACTION100
2.6071-2.80830.23441440.21232664X-RAY DIFFRACTION100
2.8083-3.09060.22561430.19552653X-RAY DIFFRACTION100
3.0906-3.53720.22251460.18832692X-RAY DIFFRACTION100
3.5372-4.45410.19321450.15882684X-RAY DIFFRACTION100
4.4541-29.60140.17971530.17352826X-RAY DIFFRACTION99

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