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- PDB-3rvt: Structure of 4C1 Fab in P212121 space group -

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Basic information

Entry
Database: PDB / ID: 3rvt
TitleStructure of 4C1 Fab in P212121 space group
Components
  • Fab fragment of 4C1 antibody - heavy chain
  • Fab fragment of 4C1 antibody - light chain
KeywordsIMMUNE SYSTEM / IgG / antibody / Der f 1 / Der p 1
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsChruszcz, M. / Vailes, L.D. / Chapman, M.D. / Pomes, A. / Minor, W.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Molecular determinants for antibody binding on group 1 house dust mite allergens.
Authors: Chruszcz, M. / Pomes, A. / Glesner, J. / Vailes, L.D. / Osinski, T. / Porebski, P.J. / Majorek, K.A. / Heymann, P.W. / Platts-Mills, T.A. / Minor, W. / Chapman, M.D.
History
DepositionMay 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Fab fragment of 4C1 antibody - light chain
D: Fab fragment of 4C1 antibody - heavy chain


Theoretical massNumber of molelcules
Total (without water)51,6152
Polymers51,6152
Non-polymers00
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-25 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.050, 79.656, 80.948
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Fab fragment of 4C1 antibody - light chain


Mass: 23937.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)
#2: Antibody Fab fragment of 4C1 antibody - heavy chain


Mass: 27677.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, 15% w/v PEG4000, 0.1M KCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2009 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 30422 / Num. obs: 30422 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 30.1
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.564 / % possible all: 98.1

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
REFMAC5.5.0109refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 9.918 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 1524 5 %RANDOM
Rwork0.19325 ---
obs0.19526 28688 99.69 %-
all-28688 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.373 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2--1.3 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 0 219 3597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223482
X-RAY DIFFRACTIONr_bond_other_d00.022318
X-RAY DIFFRACTIONr_angle_refined_deg1.681.9534751
X-RAY DIFFRACTIONr_angle_other_deg4.27135673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8215435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68124.071140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11415559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4711515
X-RAY DIFFRACTIONr_chiral_restr0.1170.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213855
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02695
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8291.52176
X-RAY DIFFRACTIONr_mcbond_other01.5873
X-RAY DIFFRACTIONr_mcangle_it1.51223551
X-RAY DIFFRACTIONr_scbond_it2.28131306
X-RAY DIFFRACTIONr_scangle_it3.4464.51200
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 105 -
Rwork0.252 2075 -
obs--98.38 %
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)
13.79440.3022-0.60333.51051.63473.7802-0.0770.1415-0.530.4444-0.09570.2930.5542-0.01980.17260.170.03880.06750.2270.010.299813.915-9.655-10.456
24.4826-0.6568-2.25143.25061.08673.1977-0.19760.2501-0.3833-0.14550.0169-0.08120.1206-0.59510.18070.0433-0.00860.02620.34850.00120.2634-18.9-0.4244.544
33.4613-0.3991-0.11311.81760.80862.188-0.0068-0.06740.02140.01010.0728-0.00150.00630.4713-0.0660.03410.00210.02330.31430.02640.172722.2416.6490.479
46.31851.9013-1.14573.44240.12292.42680.0469-0.6533-0.46930.2923-0.07370.09210.2849-0.05160.02680.10780.0346-0.00270.32280.10660.303-8.0280.38615.781
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1 - 107
2X-RAY DIFFRACTION2C108 - 212
3X-RAY DIFFRACTION3D1 - 121
4X-RAY DIFFRACTION4D122 - 222

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