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- PDB-2d03: Crystal structure of the G91S mutant of the NNA7 Fab -

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Basic information

Entry
Database: PDB / ID: 2d03
TitleCrystal structure of the G91S mutant of the NNA7 Fab
Components(anti-glycophorin A type N immunoglobulin ...) x 2
KeywordsIMMUNE SYSTEM / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsXie, K. / Song, S.C. / Spitalnik, S.L. / Wedekind, J.E.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Crystallographic analysis of the NNA7 Fab and proposal for the mode of human blood-group recognition.
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.
History
DepositionJul 23, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 2023Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: anti-glycophorin A type N immunoglobulin light chain
H: anti-glycophorin A type N immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,60711
Polymers47,6612
Non-polymers9469
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-17 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.560, 70.650, 122.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsOne L-chain and one H-chain compose the Fab fragment

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody anti-glycophorin A type N immunoglobulin light chain / FAB NNA7 light chain


Mass: 23898.514 Da / Num. of mol.: 1 / Mutation: G91S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pCOM3H / Production host: Escherichia coli (E. coli) / Strain (production host): SURE
#2: Antibody anti-glycophorin A type N immunoglobulin heavy chain / FAB NNA7 heavy chain


Mass: 23762.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pCOM3H / Production host: Escherichia coli (E. coli) / Strain (production host): SURE / References: GenBank: 68144533

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Non-polymers , 4 types, 312 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / 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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.71 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 5000 MME, (NH4)2SO4, MES, YCl3, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 4, 2004 / Details: mirrors
RadiationMonochromator: Horizontal focusing, 5.05 asymmetric cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.97→24.44 Å / Num. all: 147694 / Num. obs: 35107 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.21 % / Biso Wilson estimate: 22.4 Å2 / Rsym value: 0.07 / Net I/σ(I): 9.6
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 3.34 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4379 / Rsym value: 0.424 / % possible all: 88.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
CrystalClear(MSC/RIGAKU)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1T2Q

1t2q


Resolution: 1.97→24.44 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1788620.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3410 9.9 %RANDOM
Rwork0.218 ---
all0.221 36075 --
obs0.218 34324 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.3098 Å2 / ksol: 0.391093 e/Å3
Displacement parametersBiso mean: 41.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.02 Å20 Å20 Å2
2--12.86 Å20 Å2
3----8.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 1.97→24.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3275 0 61 303 3639
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.97→2.09 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.405 503 10.3 %
Rwork0.381 4379 -
obs-4376 82.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3gol.paramgol.top
X-RAY DIFFRACTION4mes_xplor.parammes_xplor.top
X-RAY DIFFRACTION5peg_xplor.parampeg_xplor.top

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