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- PDB-1a6t: FAB FRAGMENT OF MAB1-IA MONOCLONAL ANTIBODY TO HUMAN RHINOVIRUS 1... -

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Basic information

Entry
Database: PDB / ID: 1a6t
TitleFAB FRAGMENT OF MAB1-IA MONOCLONAL ANTIBODY TO HUMAN RHINOVIRUS 14 NIM-IA SITE
Components
  • IGG1 FAB1-IA FAB (HEAVY CHAIN)
  • IGG1 FAB1-IA FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN / NEUTRALIZES HUMAN RHINOVIRUS / IGG1
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChe, Z. / Smith, T.J.
CitationJournal: J.Virol. / Year: 1998
Title: Antibody-mediated neutralization of human rhinovirus 14 explored by means of cryoelectron microscopy and X-ray crystallography of virus-Fab complexes.
Authors: Che, Z. / Olson, N.H. / Leippe, D. / Lee, W.M. / Mosser, A.G. / Rueckert, R.R. / Baker, T.S. / Smith, T.J.
History
DepositionMar 3, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IGG1 FAB1-IA FAB (LIGHT CHAIN)
B: IGG1 FAB1-IA FAB (HEAVY CHAIN)
C: IGG1 FAB1-IA FAB (LIGHT CHAIN)
D: IGG1 FAB1-IA FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)91,9844
Polymers91,9844
Non-polymers00
Water00
1
A: IGG1 FAB1-IA FAB (LIGHT CHAIN)
B: IGG1 FAB1-IA FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)45,9922
Polymers45,9922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-26 kcal/mol
Surface area18830 Å2
MethodPISA
2
C: IGG1 FAB1-IA FAB (LIGHT CHAIN)
D: IGG1 FAB1-IA FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)45,9922
Polymers45,9922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-26 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.170, 135.950, 81.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsTHERE ARE TWO FABS IN THE ASYMMETRIC UNIT. THE LIGHT AND HEAVY CHAINS ARE CALLED A AND B, RESPECTIVELY, FOR THE FIRST AND C AND D FOR THE SECOND.

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Components

#1: Antibody IGG1 FAB1-IA FAB (LIGHT CHAIN) / IGG1 IMMUNOGLOBULIN


Mass: 22697.986 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Details: MONOCLONAL ANTIBODY / Source: (natural) Mus musculus (house mouse) / References: PIR: S25058
#2: Antibody IGG1 FAB1-IA FAB (HEAVY CHAIN) / IGG1 IMMUNOGLOBULIN


Mass: 23294.027 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Details: MONOCLONAL ANTIBODY / Source: (natural) Mus musculus (house mouse) / References: PIR: S38950
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.43 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6
Details: SITTING DROP METHOD USING 18-22% PEG8000, 0.1 M SODIUM PHOSPHATE BUFFER (PH 6.0), AND 1% 2-METHYL-2,4-PENTANEDIOL WITH AN FAB1 CONCENTRATION OF 18 MG/ML., vapor diffusion - sitting drop
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 mg/mlFab11drop
218-22 %PEG80001reservoir
30.1 Msodium phosphate1reservoir
41 %MPD1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 29406 / % possible obs: 91.7 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 3700
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 581 / Rsym value: 0.15 / % possible all: 89.2
Reflection shell
*PLUS
% possible obs: 89.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FOR

1for


Resolution: 2.7→6 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: STILL BEING REFINED
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2602 9 %RANDOM
Rwork0.169 ---
obs0.169 28915 93.3 %-
Displacement parametersBiso mean: 23.2 Å2
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7942 0 0 314 8256
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.87
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.7→2.81 Å / Total num. of bins used: 6 / % reflection obs: 92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2

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