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- PDB-5aze: Fab fragment of calcium-dependent antigen binding antibody, 6RL#9 -

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Basic information

Entry
Database: PDB / ID: 5aze
TitleFab fragment of calcium-dependent antigen binding antibody, 6RL#9
Components
  • 6RL#9 FAB HEAVY CHAIN
  • 6RL#9 FAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM / calcium-dependent / RECYCLING ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKadono, S. / Hironiwa, N. / Ishii, S. / Igawa, T. / Hattori, K.
CitationJournal: Mabs / Year: 2016
Title: Calcium-dependent antigen binding as a novel modality for antibody recycling by endosomal antigen dissociation
Authors: Hironiwa, N. / Ishii, S. / Kadono, S. / Iwayanagi, Y. / Mimoto, F. / Habu, K. / Igawa, T. / Hattori, K.
History
DepositionOct 2, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Mar 2, 2016Group: Structure summary
Revision 1.3Jun 13, 2018Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_host_org_cell_line ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 6RL#9 FAB LIGHT CHAIN
H: 6RL#9 FAB HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2623
Polymers47,2222
Non-polymers401
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-39 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.470, 79.860, 116.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody 6RL#9 FAB LIGHT CHAIN


Mass: 22789.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293F / Production host: Homo sapiens (human)
#2: Antibody 6RL#9 FAB HEAVY CHAIN


Mass: 24432.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293F / Production host: Homo sapiens (human)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCES OF THIS PROTEIN WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) ...THE SEQUENCES OF THIS PROTEIN WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20.0% PEG 4000, 0.1M HEPES

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→42.35 Å / Num. obs: 22199 / % possible obs: 99.99 % / Observed criterion σ(I): -3 / Redundancy: 7.12 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 14.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.25 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
xia2data processing
XDSdata reduction
XSCALEdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZA6 for VH, CL, and CH1 regions, 2A9M for VL region

1za6

2a9m


Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.89 / SU B: 6.947 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.325 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2724 1162 5.2 %RANDOM
Rwork0.2114 ---
obs0.2145 21023 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 59.33 Å2 / Biso mean: 27.373 Å2 / Biso min: 17.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--0.69 Å2-0 Å2
3----0.52 Å2
Refinement stepCycle: final / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3195 0 1 238 3434
Biso mean--47.71 30.37 -
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193280
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9544475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9065427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49424.336113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41415500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.516159
X-RAY DIFFRACTIONr_chiral_restr0.0680.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212447
X-RAY DIFFRACTIONr_mcbond_it0.8212.7031717
X-RAY DIFFRACTIONr_mcangle_it1.4964.0512141
X-RAY DIFFRACTIONr_scbond_it0.6812.7051563
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 97 -
Rwork0.254 1494 -
all-1591 -
obs--100 %

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