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- PDB-1t2q: The Crystal Structure of an NNA7 Fab that recognizes an N-type bl... -

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Basic information

Entry
Database: PDB / ID: 1t2q
TitleThe Crystal Structure of an NNA7 Fab that recognizes an N-type blood group antigen
Components
  • Fab NNA7 Heavy Chain
  • Fab NNA7 Light Chain
KeywordsIMMUNE SYSTEM / Fab / glycophorin A / blood group antigen
Function / homology
Function and homology information


phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin complex / immunoglobulin mediated immune response / complement activation, classical pathway ...phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin complex / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding / positive regulation of phagocytosis / B cell differentiation / positive regulation of immune response / antibacterial humoral response / adaptive immune response / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular region / metal ion binding / cytoplasm
Similarity search - Function
: / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin ...: / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
If kappa light chain / Immunoglobulin heavy variable 2-4 / Ig gamma-1 chain C region secreted form
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsXie, K. / Song, S.C. / Spitalnik, S.L. / Wedekind, J.E.
Citation
Journal: To be Published
Title: Crystal Structure and Mutational Analysis of an Antibody that Recognizes an N-type Blood Group Antigen
Authors: Xie, K. / Song, S.C. / Spitalnik, S.L. / Wedekind, J.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Purification, Crystallization and X-ray Diffraction Analysis of a Recombinant Fab that Recognizes a Human Blood Group antigen
Authors: Song, S.C. / Xie, K. / Czerwinski, M. / Spitalnik, S.L. / Wedekind, J.E.
#2: Journal: Transfusion / Year: 2004
Title: Alteration of Amino Acid Residues at the L-chain N-terminus and in Complementarity-Determining Region 3 Increases Affinity of a Recombinant F(ab) for the Human N Blood Group Antigen
Authors: Song, S.C. / Czerwinski, M. / Wojczyk, B.S. / Spitalnik, S.L.
History
DepositionApr 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE The sequence of the protein was not deposited into any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab NNA7 Heavy Chain
H: Fab NNA7 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8225
Polymers47,4432
Non-polymers3793
Water11,025612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-22 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.863, 77.123, 118.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit comprises the heavy and light chains that form the Fab fragment

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Components

#1: Antibody Fab NNA7 Heavy Chain


Mass: 23868.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Monoclonal Antibody / Gene: N92 IgG2a / Plasmid: pComb3H / Production host: Escherichia coli (E. coli) / Strain (production host): SURE / References: UniProt: A2NHM3*PLUS
#2: Antibody Fab NNA7 Light Chain


Mass: 23574.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: phage display modified / Gene: N92 L chain / Plasmid: pComb3H / Production host: Escherichia coli (E. coli) / Strain (production host): SURE / References: UniProt: P01868, UniProt: P01821*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 2.8 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG MME 5K, ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 11, 2003 / Details: Osmic Confocal Blue
RadiationMonochromator: Confocal Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.83→36.7 Å / Num. obs: 43775 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 22.2 Å2 / Rsym value: 0.065 / Net I/σ(I): 12.9
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.293 / % possible all: 53

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
AMoRE(STAND ALONE)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 48G7

48g7


Resolution: 1.83→36.6 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3465 7.9 %RANDOM
Rwork0.204 ---
obs0.204 43775 92.3 %-
all-43775 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.3753 Å2 / ksol: 0.385562 e/Å3
Displacement parametersBiso mean: 29.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.79 Å20 Å20 Å2
2--5.46 Å20 Å2
3----2.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati sigma a0.32 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.83→36.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 24 612 3922
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d27.5
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.572
X-RAY DIFFRACTIONc_mcangle_it2.22.5
X-RAY DIFFRACTIONc_scbond_it2.32.5
X-RAY DIFFRACTIONc_scangle_it3.233
LS refinement shellResolution: 1.83→1.94 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 468 10 %
Rwork0.336 4224 -
obs-4224 60.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3GOL_XPLOR_PARGOL_XPLOR_TOP
X-RAY DIFFRACTION4MES_XPLOR_PARMES_XPLOR_TOP

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