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- PDB-4a6y: CRYSTAL STRUCTURE OF FAB FRAGMENT OF ANTI-(4-HYDROXY-3-NITROPHENY... -

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Basic information

Entry
Database: PDB / ID: 4a6y
TitleCRYSTAL STRUCTURE OF FAB FRAGMENT OF ANTI-(4-HYDROXY-3-NITROPHENYL) -ACETYL MURINE GERMLINE ANTIBODY BBE6.12H3
Components
  • (ANTIBODY BBE6.12H3 HEAVY CHAIN) x 2
  • (ANTIBODY BBE6.12H3 LIGHT CHAIN) x 2
KeywordsIMMUNE SYSTEM / ANTIBODY MULTISPECIFICITY / HUMORAL IMMUNE SYSTEM / COMPLEMENTARITY DETERMINING REGION FLEXIBILITY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKhan, T. / Salunke, D.M.
CitationJournal: J.Immunol. / Year: 2012
Title: Structural Elucidation of the Mechanistic Basis of Degeneracy in the Primary Humoral Response.
Authors: Khan, T. / Salunke, D.M.
History
DepositionNov 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.2Nov 13, 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: ANTIBODY BBE6.12H3 LIGHT CHAIN
B: ANTIBODY BBE6.12H3 HEAVY CHAIN
H: ANTIBODY BBE6.12H3 HEAVY CHAIN
L: ANTIBODY BBE6.12H3 LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)92,8884
Polymers92,8884
Non-polymers00
Water2,342130
1
A: ANTIBODY BBE6.12H3 LIGHT CHAIN
B: ANTIBODY BBE6.12H3 HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)46,4302
Polymers46,4302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-26.2 kcal/mol
Surface area19090 Å2
MethodPISA
2
H: ANTIBODY BBE6.12H3 HEAVY CHAIN
L: ANTIBODY BBE6.12H3 LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)46,4582
Polymers46,4582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-24.1 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.283, 81.418, 128.911
Angle α, β, γ (deg.)90.00, 90.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody ANTIBODY BBE6.12H3 LIGHT CHAIN


Mass: 22681.086 Da / Num. of mol.: 1 / Fragment: ANTIGEN BINDING / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B CELL / Cell line: ANTI-NP MURINE HYBRIDOMA / Organ: SPLEEN / Strain: C57BL/6
#2: Antibody ANTIBODY BBE6.12H3 HEAVY CHAIN


Mass: 23748.617 Da / Num. of mol.: 1 / Fragment: ANTIGEN BINDING / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B CELL / Cell line: ANTI-NP MURINE HYBRIDOMA / Organ: SPLEEN / Strain: C57BL/6
#3: Antibody ANTIBODY BBE6.12H3 HEAVY CHAIN


Mass: 23762.643 Da / Num. of mol.: 1 / Fragment: ANTIGEN BINDING / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B CELL / Cell line: ANTI-NP MURINE HYBRIDOMA / Organ: SPLEEN / Strain: C57BL/6
#4: Antibody ANTIBODY BBE6.12H3 LIGHT CHAIN


Mass: 22695.174 Da / Num. of mol.: 1 / Fragment: ANTIGEN BINDING / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B CELL / Cell line: ANTI-NP MURINE HYBRIDOMA / Organ: SPLEEN / Strain: C57BL/6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.3 Å3/Da / Density % sol: 45.7 % / Description: NONE
Crystal growpH: 7.1 / Details: 21% PEG 3350 IN 0.05 M TRIS, PH 7.1

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 2006 / Details: MIRRORS
RadiationMonochromator: NI FILTER CMF12 38CU-6 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 19688 / % possible obs: 93.5 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.7
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.6 / % possible all: 87.3

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Processing

Software
NameVersionClassification
CNS1.2refinement
AUTOMARdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NGQ

1ngq


Resolution: 2.9→23.02 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 125478.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1665 9.9 %RANDOM
Rwork0.24 ---
obs0.24 16819 84.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.3416 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å20 Å2-1.44 Å2
2--8.46 Å20 Å2
3----6.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 2.9→23.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6463 0 0 130 6593
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.45
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.071.5
X-RAY DIFFRACTIONc_mcangle_it3.412
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.882.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 233 9.1 %
Rwork0.355 2328 -
obs--76.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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