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- PDB-6al4: CRYSTAL STRUCTURE OF ANTI-CD19 ANTIBODY B43 FAB -

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Basic information

Entry
Database: PDB / ID: 6al4
TitleCRYSTAL STRUCTURE OF ANTI-CD19 ANTIBODY B43 FAB
Components
  • B43 HEAVY CHAIN
  • B43 LIGHT CHAIN
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


immunoglobulin complex / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IGH@ protein / IGK@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsTeplyakov, A. / Obmolova, G. / Gilliland, G.L.
CitationJournal: Proteins / Year: 2018
Title: Crystal structure of B-cell co-receptor CD19 in complex with antibody B43 reveals an unexpected fold.
Authors: Teplyakov, A. / Obmolova, G. / Luo, J. / Gilliland, G.L.
History
DepositionAug 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: B43 LIGHT CHAIN
B: B43 HEAVY CHAIN
C: B43 LIGHT CHAIN
D: B43 HEAVY CHAIN
E: B43 LIGHT CHAIN
F: B43 HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)147,1216
Polymers147,1216
Non-polymers00
Water5,945330
1
A: B43 LIGHT CHAIN
B: B43 HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)49,0402
Polymers49,0402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-27 kcal/mol
Surface area20300 Å2
MethodPISA
2
C: B43 LIGHT CHAIN
D: B43 HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)49,0402
Polymers49,0402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-26 kcal/mol
Surface area20090 Å2
MethodPISA
3
E: B43 LIGHT CHAIN
F: B43 HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)49,0402
Polymers49,0402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-26 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.100, 127.360, 219.390
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 B43 LIGHT CHAIN


Mass: 23815.260 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGK@ / Production host: Homo sapiens (human) / References: UniProt: Q6P5S8
#2: Antibody B43 HEAVY CHAIN


Mass: 25225.055 Da / Num. of mol.: 3 / Fragment: FD,FD,FD,FD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGH@ / Production host: Homo sapiens (human) / References: UniProt: Q6GMX6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 3.47 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.1 / Details: 20% PEG 3350, 0.2 M NA PHOSPHATE DIBASIC / PH range: 9.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 80381 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 52.2 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 22.3
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 7505 / % possible all: 91.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0049refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5i15

5i15


Resolution: 2.45→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.759 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.223
RfactorNum. reflection% reflectionSelection details
Rfree0.23642 1455 2 %RANDOM
Rwork0.20581 ---
obs0.20645 72582 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 60.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å2-0 Å2
2--0.73 Å2-0 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10063 0 0 330 10393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0210317
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0161.94814061
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.52551316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7924.693407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.556151617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6071533
X-RAY DIFFRACTIONr_chiral_restr0.0640.21572
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217801
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.7617.9155285
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.47717.7876594
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8288.0995032
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.24814897
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 89 -
Rwork0.301 4992 -
obs--92.8 %

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