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- PDB-3qo1: Monoclinic form of IgG1 Fab fragment (apo form) sharing same Fv as IgA -

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Basic information

Entry
Database: PDB / ID: 3qo1
TitleMonoclinic form of IgG1 Fab fragment (apo form) sharing same Fv as IgA
Components
  • Fab fragment of IMMUNOGLOBULIN G1 HEAVY CHAIN
  • Fab fragment of IMMUNOGLOBULIN G1 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / immunoglobulin fold / antibody / serum
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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 G1 LIGHT CHAIN
B: Fab fragment of IMMUNOGLOBULIN G1 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3944
Polymers47,2102
Non-polymers1842
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-22 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.297, 67.214, 68.952
Angle α, β, γ (deg.)90.000, 103.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab fragment of IMMUNOGLOBULIN G1 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 G1 HEAVY CHAIN


Mass: 23200.025 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.54 Å3/Da / Density % sol: 51.67 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Na citrate, 20% isopropanol, 16% PEG 4000, pH 5.5, 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: Nov 26, 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: 2.4→67.214 Å / Num. all: 18623 / Num. obs: 18623 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 43.59 Å2 / Rsym value: 0.092 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.3 %

Resolution (Å)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.4-2.530.5910.4971.5876426950.3160.5910.4972.7100
2.53-2.680.4450.3742.1844725900.2380.4450.3743.6100
2.68-2.870.3080.263783223840.1640.3080.264.9100
2.87-3.10.1960.1654.7743822550.1050.1960.1657100
3.1-3.390.1170.0987.8685120730.0620.1170.09811.2100
3.39-3.790.0780.06511.5625618870.0420.0780.06516.7100
3.79-4.380.0590.04914.3551516600.0310.0590.04921100
4.38-5.370.0450.03818.4472614250.0240.0450.03824.7100
5.37-7.590.050.04316.6360810850.0270.050.04320.899.3
7.59-19.2840.0320.02723.218885690.0170.0320.0273092

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data 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

2eh7


Resolution: 2.4→19.28 Å / Cor.coef. Fo:Fc: 0.9423 / Cor.coef. Fo:Fc free: 0.9018 / 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 has been employed
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 879 4.72 %RANDOM
Rwork0.1661 ---
all0.1687 18608 --
obs0.1687 18608 99.65 %-
Displacement parametersBiso max: 115.68 Å2 / Biso mean: 31.9804 Å2 / Biso min: 10.82 Å2
Baniso -1Baniso -2Baniso -3
1-6.7149 Å20 Å20.2114 Å2
2--0.8284 Å20 Å2
3----7.5433 Å2
Refine analyzeLuzzati coordinate error obs: 0.267 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3301 0 12 185 3498
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013381HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.284588HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1148SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes494HARMONIC5
X-RAY DIFFRACTIONt_it3381HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.66
X-RAY DIFFRACTIONt_other_torsion20.27
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion446SEMIHARMONIC5
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_contact3805SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.54 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2783 138 4.61 %
Rwork0.2016 2858 -
all0.2052 2996 -
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)
11.22240.05190.06260.1805-0.24181.75220.04130.1612-0.0106-0.0345-0.06080.00030.06970.1240.0194-0.05690.0232-0.0001-0.0136-0.0127-0.008126.589-5.374112.7
22.1346-0.026-0.37480.91650.2910.61090.0069-0.1083-0.01570.1121-0.0021-0.03940.01480.0072-0.0047-0.031-0.0077-0.0018-0.03870.0065-0.0186-0.2487-4.58639.5595
31.72390.2488-0.87381.4164-0.46151.92530.00310.12260.128-0.096-0.07460.0356-0.0159-0.05390.0715-0.0616-0.0022-0.0326-0.026-0.0028-0.0288.97632.05390.5201
40.98030.14230.19381.1080.50440.78780.0418-0.0939-0.03020.0187-0.0493-0.1104-0.0793-0.07330.0075-0.0369-0.01450.0093-0.04840.01630.0116-1.6617.96130.0179
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|2 - B|119 }B2 - 119
4X-RAY DIFFRACTION4{ B|120 - B|220 }B120 - 220

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