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

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Basic information

Entry
Database: PDB / ID: 3qny
TitleMonoclinic 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 / molecular replacement / Resolution: 2.3 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 9, 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
C: FAB FRAGMENT OF IMMUNOGLOBULIN A1 LIGHT CHAIN
D: FAB FRAGMENT OF IMMUNOGLOBULIN A1 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2166
Polymers95,0324
Non-polymers1842
Water4,414245
1
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)47,7004
Polymers47,5162
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-25 kcal/mol
Surface area18680 Å2
MethodPISA
2
C: FAB FRAGMENT OF IMMUNOGLOBULIN A1 LIGHT CHAIN
D: FAB FRAGMENT OF IMMUNOGLOBULIN A1 HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)47,5162
Polymers47,5162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-25 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.300, 50.000, 99.200
Angle α, β, γ (deg.)90.000, 107.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody FAB FRAGMENT OF IMMUNOGLOBULIN A1 LIGHT CHAIN


Mass: 24009.725 Da / Num. of mol.: 2 / 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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.2M potassium sulfate, 20% PEG 3350, pH 8.2, 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: Aug 11, 2008
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: 2.3→27.5 Å / Num. all: 39517 / Num. obs: 39517 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 41.948 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.44
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.3-2.40.5640.4483.1614719480943850.52791.2
2.4-2.60.40.3234.325598755273260.37997
2.6-2.80.2350.1886.619506557054350.22197.6
2.8-30.1380.1229.7614943419641380.14398.6
3-3.50.0680.06616.0524437675966770.07898.8
3.5-40.0410.04822.7213680379937590.05698.9
4-7.070.030.03627.2922931641963540.04299
7.07-100.0290.03529.6633129579430.04298.5
10-27.50.0250.03330.816655455000.03991.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
AMoREphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XDSdata reduction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EH7 (for the light chains) and 2FBJ (for the heavy chains)

2eh7

2fbj


Resolution: 2.3→18.75 Å / Cor.coef. Fo:Fc: 0.9315 / Cor.coef. Fo:Fc free: 0.9132 / Occupancy max: 1 / Occupancy min: 1 / 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
Rfree0.2178 1220 3.09 %RANDOM
Rwork0.1868 ---
all0.1878 39455 --
obs0.1878 39455 97.28 %-
Displacement parametersBiso max: 147.75 Å2 / Biso mean: 50.16 Å2 / Biso min: 15.46 Å2
Baniso -1Baniso -2Baniso -3
1-6.0502 Å20 Å20.3168 Å2
2--2.4517 Å20 Å2
3----8.5019 Å2
Refine analyzeLuzzati coordinate error obs: 0.317 Å
Refinement stepCycle: LAST / Resolution: 2.3→18.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6305 0 12 245 6562
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2089SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes139HARMONIC2
X-RAY DIFFRACTIONt_gen_planes955HARMONIC5
X-RAY DIFFRACTIONt_it6461HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion882SEMIHARMONIC5
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_contact7475SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6461HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8816HARMONIC21.24
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion17.91
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2687 84 3.19 %
Rwork0.2161 2553 -
all0.2178 2637 -
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)
17.8694-1.23761.41662.8785-1.03533.817-0.0021-0.6827-0.38990.407-0.352-0.440.01290.35540.3542-0.3026-0.0613-0.02070.13930.1314-0.1859-42.8153-19.2577-9.2278
22.0903-0.0349-0.86521.086-0.09891.23310.15980.05430.1301-0.2532-0.0443-0.017-0.1096-0.2368-0.1155-0.0270.01290.0407-0.09320.0191-0.0052-46.0492-7.8558-44.7403
32.2074-0.2729-1.09561.9244-0.3024.84960.0585-0.6570.01720.24210.3150.0411-0.19450.2739-0.3735-0.26390.00810.00720.1595-0.0235-0.0814-20.7265-15.8099-15.142
41.87050.6274-0.30041.9567-0.0321.17060.2128-0.17030.28460.0913-0.12240.1577-0.1862-0.0861-0.0905-0.0418-0.02270.0832-0.124-0.02320.0494-35.71311.2106-37.231
58.8013-1.9171-1.07962.69051.40823.7817-0.0417-0.3885-0.02760.177-0.33260.3453-0.2272-0.57760.3743-0.3131-0.0323-0.00240.2055-0.0612-0.1967-72.0701-18.5924-9.4189
62.22340.04520.66571.32040.15091.53540.18140.0104-0.0935-0.2153-0.0690.04530.13750.2238-0.1124-0.07030.0183-0.0367-0.1172-0.01980.0384-68.5001-30.389-44.599
70.80241.01280.23631.6721.90975.62820.1082-0.4531-0.34430.20490.03370.08370.234-0.3728-0.1419-0.3369-0.00410.00450.16140.1198-0.0011-94.0347-22.1554-15.9593
82.05380.12010.50752.5459-0.35831.39930.16-0.1915-0.24610.1594-0.0691-0.09310.13820.0583-0.091-0.0716-0.0201-0.0939-0.15980.01680.1066-79.3162-39.4212-37.1311
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|114 }A2 - 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
5X-RAY DIFFRACTION5{ C|1 - C|114 }C1 - 114
6X-RAY DIFFRACTION6{ C|115 - C|219 }C115 - 219
7X-RAY DIFFRACTION7{ D|4 - D|119 }D4 - 119
8X-RAY DIFFRACTION8{ D|120 - D|221 }D120 - 221

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