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- PDB-3qnx: Orthorhombic form of human IgA1 Fab fragment, sharing same Fv as IgG -

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Basic information

Entry
Database: PDB / ID: 3qnx
TitleOrthorhombic form of human IgA1 Fab fragment, sharing same Fv as IgG
Components
  • Fab fragment of IMMUNOGLOBULIN A1 HEAVY CHAIN
  • Fab fragment of IMMUNOGLOBULIN A1 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / immunoglobulin fold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTrajtenberg, F. / Correa, A. / Buschiazzo, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of a human IgA1 Fab fragment at 1.55 angstrom resolution: potential effect of the constant domains on antigen-affinity modulation
Authors: Correa, A. / Trajtenberg, F. / Obal, G. / Pritsch, O. / Dighiero, G. / Oppezzo, P. / Buschiazzo, A.
History
DepositionFeb 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 1, 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 1.4Oct 30, 2024Group: Structure summary / Category: 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: Fab fragment of IMMUNOGLOBULIN A1 LIGHT CHAIN
B: Fab fragment of IMMUNOGLOBULIN A1 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7925
Polymers47,5162
Non-polymers2763
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-22 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.780, 95.850, 107.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-229-

HOH

21A-270-

HOH

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Components

#1: Antibody Fab fragment of IMMUNOGLOBULIN A1 LIGHT CHAIN


Mass: 24009.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: serum / Source: (natural) Homo sapiens (human)
#2: Antibody Fab fragment of IMMUNOGLOBULIN A1 HEAVY CHAIN


Mass: 23506.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: serum / Source: (natural) Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.69 Å3/Da / Density % sol: 54.33 % / Mosaicity: 0.58 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.8
Details: 1.8M (NH4)2SO4, 0.1M PO4/citrate, pH 3.8, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 18, 2009
RadiationMonochromator: Varimax-HF multilayer mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→47.925 Å / Num. all: 26858 / Num. obs: 26858 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 33.23 Å2 / Rsym value: 0.104 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.323.50.580.491.61343538610.3050.580.492.6100
2.32-2.463.50.480.4061.91282236550.2530.480.4063.1100
2.46-2.633.50.3510.2982.61217134410.1840.3510.2984.1100
2.63-2.843.60.2650.2253.51132331850.1390.2650.2255.5100
2.84-3.113.60.1630.1395.61069529990.0850.1630.1398.5100
3.11-3.483.60.0940.089.6958226800.0490.0940.0813.8100
3.48-4.023.60.0670.05713.1856023990.0350.0670.05718.4100
4.02-4.923.50.050.04217730420630.0260.050.04223.7100
4.92-6.963.50.0530.04515.6563116170.0280.0530.04520.7100
6.96-47.9253.20.0470.0414.830879580.0250.0470.0422.899.3

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
AMoREphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M8O

3m8o


Resolution: 2.2→18.15 Å / Cor.coef. Fo:Fc: 0.9348 / Cor.coef. Fo:Fc free: 0.9102 / Occupancy max: 1 / Occupancy min: 0.3 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: TLS refinement was performed
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 1352 5.05 %RANDOM
Rwork0.1815 ---
all0.1837 26771 --
obs0.1837 26771 99.75 %-
Displacement parametersBiso max: 121.1 Å2 / Biso mean: 33.7879 Å2 / Biso min: 9.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.4372 Å20 Å20 Å2
2--4.1694 Å20 Å2
3----5.6066 Å2
Refine analyzeLuzzati coordinate error obs: 0.257 Å
Refinement stepCycle: LAST / Resolution: 2.2→18.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3288 0 18 234 3540
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1135SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes79HARMONIC2
X-RAY DIFFRACTIONt_gen_planes494HARMONIC5
X-RAY DIFFRACTIONt_it3387HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion450SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3833SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3387HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4607HARMONIC21.22
X-RAY DIFFRACTIONt_omega_torsion3.46
X-RAY DIFFRACTIONt_other_torsion18.1
LS refinement shellResolution: 2.2→2.29 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2289 150 5.05 %
Rwork0.1966 2823 -
all0.1983 2973 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.74890.26150.00153.3782-0.21870.8691-0.23120.11880.0861-0.54420.23480.2805-0.049-0.0917-0.00360.1226-0.0655-0.0694-0.08850.0209-0.08820.839714.486215.1588
20.52660.1830.29781.31111.29241.0716-0.01310.0025-0.11310.02110.0406-0.07680.07550.0478-0.0275-0.0237-0.00470.0111-0.02180.01410.020513.483811.35250.76
31.8944-0.3330.48372.9350.46712.2606-0.01290.24260.1096-0.54420.0996-0.1926-0.0090.0625-0.08660.0548-0.00950.0632-0.0930.0314-0.05516.602436.29419.3626
41.7469-0.25660.0080.9963-0.21120.6034-0.02480.1147-0.07-0.0858-0.0018-0.0613-0.013-0.07370.0266-0.06310.00070.0136-0.0435-0.0046-0.009822.757121.584543.3037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|114 }A1 - 114
2X-RAY DIFFRACTION2{ A|115 - A|219 }A115 - 219
3X-RAY DIFFRACTION3{ B|3 - B|119 }B3 - 119
4X-RAY DIFFRACTION4{ B|120 - B|221 }B120 - 221

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