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- PDB-4poz: Fab fragment of Der p 1 specific antibody 10B9 -

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Basic information

Entry
Database: PDB / ID: 4poz
TitleFab fragment of Der p 1 specific antibody 10B9
Components
  • heavy chain of Fab fragment of 10B9 antibody
  • light chain of Fab fragment of 10B9 antibody
KeywordsIMMUNE SYSTEM / antibody / allergy
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsOsinski, T. / Majorek, K.A. / Pomes, A. / Offermann, L.R. / Osinski, S. / Glesner, J. / Vailes, L.D. / Chapman, M.D. / Minor, W. / Chruszcz, M.
CitationJournal: J. Immunol. / Year: 2015
Title: Structural Analysis of Der p 1-Antibody Complexes and Comparison with Complexes of Proteins or Peptides with Monoclonal Antibodies.
Authors: Osinski, T. / Pomes, A. / Majorek, K.A. / Glesner, J. / Offermann, L.R. / Vailes, L.D. / Chapman, M.D. / Minor, W. / Chruszcz, M.
History
DepositionFeb 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Apr 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 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 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
C: light chain of Fab fragment of 10B9 antibody
D: heavy chain of Fab fragment of 10B9 antibody


Theoretical massNumber of molelcules
Total (without water)47,4162
Polymers47,4162
Non-polymers00
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-26 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.020, 121.829, 55.041
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody light chain of Fab fragment of 10B9 antibody


Mass: 23280.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: MUS MUSCULUS (house mouse) / Strain (production host): HYBRIDOMA
#2: Antibody heavy chain of Fab fragment of 10B9 antibody


Mass: 24135.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: MUS MUSCULUS (house mouse) / Strain (production host): HYBRIDOMA
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM sodium citrate, 15% w/v PEG 6000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 11, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 45773 / Num. obs: 45773 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 27
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.633 / % possible all: 96.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
REFMAC5.8.0049refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RVT

3rvt


Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20587 2318 5.1 %RANDOM
Rwork0.16878 ---
obs0.17065 43428 98.94 %-
all-43428 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.238 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0 Å2
2---1.04 Å2-0 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3291 0 0 445 3736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023458
X-RAY DIFFRACTIONr_bond_other_d00.023120
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.9524736
X-RAY DIFFRACTIONr_angle_other_deg3.79137242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0665445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66424.211133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44215553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1021513
X-RAY DIFFRACTIONr_chiral_restr0.1240.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213958
X-RAY DIFFRACTIONr_gen_planes_other0.020.02777
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_it1.2881.1711756
X-RAY DIFFRACTIONr_mcbond_other1.2881.171755
X-RAY DIFFRACTIONr_mcangle_it1.9031.7472209
X-RAY DIFFRACTIONr_mcangle_other1.8341.9322210
X-RAY DIFFRACTIONr_scbond_it2.5091.4191702
X-RAY DIFFRACTIONr_scbond_other2.4121.5341702
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6662.1982527
X-RAY DIFFRACTIONr_long_range_B_refined6.60312.3814096
X-RAY DIFFRACTIONr_long_range_B_other6.35311.3423884
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 167 -
Rwork0.254 3057 -
obs--95.67 %
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)
11.2874-0.2231-0.76951.1682-0.00131.57260.0322-0.10640.04950.06850.0104-0.071-0.03840.021-0.04250.01050.0099-0.01740.1039-0.01070.087713.85-31.139-18.301
22.4318-0.29110.19471.4417-0.4680.8929-0.0383-0.06790.02980.1478-0.01680.09750.03850.00620.05510.0387-0.0020.0030.1185-0.00660.0927-20.819-20.656-9.418
32.082-1.50420.51372.0412-0.52280.53840.06940.1690.2433-0.1482-0.1619-0.33790.02320.05810.09240.01340.01680.02440.08360.01210.154214.716-11.999-28.884
41.46040.4749-0.2291.6339-0.34231.95030.1267-0.26630.0490.2594-0.0590.0888-0.0578-0.0584-0.06770.0435-0.02240.01010.1198-0.00450.1279-11.433-7.676-9.65
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1 - 108
2X-RAY DIFFRACTION2C109 - 211
3X-RAY DIFFRACTION3D1 - 122
4X-RAY DIFFRACTION4D123 - 222

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