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- PDB-3rvu: Structure of 4C1 Fab in C2221 space group -

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Basic information

Entry
Database: PDB / ID: 3rvu
TitleStructure of 4C1 Fab in C2221 space group
Components
  • 4C1 Fab - heavy chain
  • 4C1 Fab - 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: 2.5 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
Revision 1.3Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,6152
Polymers51,6152
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-20 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.130, 122.032, 99.703
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-265-

HOH

21D-268-

HOH

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Components

#1: Antibody 4C1 Fab - 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) / Gene: Gm16939 / Cell line (production host): HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)
#2: Antibody 4C1 Fab - 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 / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl, 15% w/v PEG4000, 0.1M NaCl, pH 8.0, 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: 2.5→50 Å / Num. all: 16631 / Num. obs: 16631 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 35.9
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.497 / % possible all: 98.8

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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
Starting model: pdb entry 3RVT

3rvt


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 29.847 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R: 0.669 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26685 836 5 %RANDOM
Rwork0.21117 ---
obs0.21399 15774 99.83 %-
all-15774 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.849 Å2
Baniso -1Baniso -2Baniso -3
1-7.09 Å20 Å20 Å2
2---3.39 Å20 Å2
3----3.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 0 33 3385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223453
X-RAY DIFFRACTIONr_bond_other_d0.0020.022288
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9534714
X-RAY DIFFRACTIONr_angle_other_deg2.27235597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6715432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17623.942137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53615546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7691515
X-RAY DIFFRACTIONr_chiral_restr0.0910.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213826
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02692
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_it0.7071.52166
X-RAY DIFFRACTIONr_mcbond_other0.0651.5869
X-RAY DIFFRACTIONr_mcangle_it1.2623532
X-RAY DIFFRACTIONr_scbond_it1.69831287
X-RAY DIFFRACTIONr_scangle_it2.6474.51182
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 62 -
Rwork0.336 1157 -
obs--99.11 %
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)
11.82040.7699-1.14865.0145-0.076.5223-0.2695-0.0378-0.1216-0.6008-0.2252-0.23420.37560.37020.49470.6625-0.0190.04320.2760.02640.1788-17.452-10.252-29.168
23.54530.8818-0.51545.00640.10126.13430.5632-0.28790.2184-0.4891-0.66710.22190.5035-0.80650.10380.9572-0.0224-0.01380.3309-0.06870.164-32.053-39.379-12.187
31.46121.274-3.85014.3973-2.345413.3550.4593-0.2202-0.10450.1495-0.41440.3229-2.05390.2217-0.0450.73290.0113-0.05550.531-0.04490.4573-23.9081.114-12.433
43.0714-2.5949-1.047810.36581.22954.89940.3229-0.54580.37210.40190.0225-0.30760.17240.1212-0.34540.6975-0.19380.04220.2913-0.07780.1799-22.871-34.742-0.481
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1 - 107
2X-RAY DIFFRACTION2C108 - 212
3X-RAY DIFFRACTION3D2 - 121
4X-RAY DIFFRACTION4D122 - 222

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