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- PDB-1jv5: Anti-blood group A Fv -

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Basic information

Entry
Database: PDB / ID: 1jv5
TitleAnti-blood group A Fv
Components
  • Ig chain heavy chain precursor V region
  • Ig kappa chain precursor V region
KeywordsImmune System / Sugar Binding Protein / immunoglobulin
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Immunoglobulin kappa variable 1-33
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsThomas, R. / Patenaude, S.I. / MacKenzie, C.R. / To, R. / Hirama, T. / Young, N.M. / Evans, S.V.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Structure of an anti-blood group A Fv and improvement of its binding affinity without loss of specificity.
Authors: Thomas, R. / Patenaude, S.I. / MacKenzie, C.R. / To, R. / Hirama, T. / Young, N.M. / Evans, S.V.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Production, crystallization and diffraction to atomic resolution of an antibody Fv specific for the blood-group A oligosaccharide antigen
Authors: Patenaude, S.I. / MacKenzie, C.R. / Bilous, D. / To, R.J. / Ryan, S.E. / Young, N.M. / Evans, S.V.
History
DepositionAug 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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
A: Ig kappa chain precursor V region
B: Ig chain heavy chain precursor V region


Theoretical massNumber of molelcules
Total (without water)24,6862
Polymers24,6862
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-10 kcal/mol
Surface area10340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.71, 57.96, 83.58
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Ig kappa chain precursor V region


Mass: 11809.013 Da / Num. of mol.: 1 / Fragment: anti-blood group A Fv
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pUCE8 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P01594
#2: Antibody Ig chain heavy chain precursor V region


Mass: 12877.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pUCE8 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: GenBank: 90683
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, HEPES, Calcium Chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Details: Patenaude, S.I., (1998) Acta Crystallogr., Sect.D, 54, 1456.
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17 mg/mlFv1drop
225-30 %PEG40001reservoir
30.1 MHEPES1reservoirpH8.0
410 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.54 Å
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Oct 15, 1994
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 12350 / Num. obs: 12350 / % possible obs: 93 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.1
Reflection shellResolution: 2.2→2.31 Å / Rmerge(I) obs: 0.073 / Mean I/σ(I) obs: 9.3 / Num. unique all: 674 / % possible all: 71.8
Reflection
*PLUS
Num. obs: 12348 / Num. measured all: 24752 / Rmerge(I) obs: 0.1

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Processing

Software
NameVersionClassification
CAD4data collection
ROTAVATAdata reduction
MERLOTphasing
X-PLOR3.1refinement
CAD4data reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→6 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.223 1266 random
Rwork0.183 --
all0.243 11626 -
obs0.183 9440 -
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2145 0 0 186 2331
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.412
LS refinement shellResolution: 2.2→3.21 Å
RfactorNum. reflection% reflection
Rfree0.256 59 -
Rwork0.203 --
obs-674 71.8 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 6 Å / Num. reflection all: 12348 / σ(F): 3
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.256 / Rfactor Rwork: 0.203

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