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- PDB-2ojz: Anti-DNA antibody ED10 -

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Basic information

Entry
Database: PDB / ID: 2ojz
TitleAnti-DNA antibody ED10
Components
  • Fab ED10 heavy chain
  • Fab ED10 light chain
KeywordsIMMUNE SYSTEM / immunoglobulin fold
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / metal ion binding
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 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
Mc5 VHCH1 / If kappa light chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsStanfield, R.L. / Sanguineti, S. / Wilson, I.A. / de Prat-Gay, G.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Specific recognition of a DNA immunogen by its elicited antibody
Authors: Sanguineti, S. / Centeno Crowley, J.M. / Lodeiro Merlo, M.F. / Cerutti, M.L. / Wilson, I.A. / Goldbaum, F.A. / Stanfield, R.L. / de Prat-Gay, G.
History
DepositionJan 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE Currently, there is no aminoacid database reference available for the proteins

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab ED10 light chain
H: Fab ED10 heavy chain
M: Fab ED10 light chain
I: Fab ED10 heavy chain


Theoretical massNumber of molelcules
Total (without water)95,2804
Polymers95,2804
Non-polymers00
Water36020
1
L: Fab ED10 light chain
H: Fab ED10 heavy chain


Theoretical massNumber of molelcules
Total (without water)47,6402
Polymers47,6402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-22 kcal/mol
Surface area19760 Å2
MethodPISA
2
M: Fab ED10 light chain
I: Fab ED10 heavy chain


Theoretical massNumber of molelcules
Total (without water)47,6402
Polymers47,6402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-23 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.899, 194.045, 61.174
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21M
12H
22I

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPLYSLYS1LA1 - 1071 - 112
221ASPASPLYSLYS1MC1 - 1071 - 112
131ARGARGGLUGLU2LA108 - 213113 - 218
241ARGARGGLUGLU2MC108 - 213113 - 218
112GLUGLUSERSER1HB1 - 1131 - 116
222GLUGLUSERSER1ID1 - 1131 - 116
132ALAALAARGARG2HB114 - 228117 - 216
242ALAALAARGARG2ID114 - 228117 - 216

NCS ensembles :
IDDetails
1L M
2H I

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Components

#1: Antibody Fab ED10 light chain


Mass: 24148.764 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A2NHM3*PLUS
#2: Antibody Fab ED10 heavy chain


Mass: 23491.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A0N7J2*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium sulfate, 0.1M sodium cacodylate, 25% MPEG 2000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.73→25.4 Å / Num. all: 27701 / Num. obs: 27701 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 47.2 Å2 / Rsym value: 11 / Net I/σ(I): 16
Reflection shellResolution: 2.73→2.8 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 2699 / Rsym value: 45.3 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ggi

1ggi


Resolution: 2.73→25.24 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.883 / SU B: 27.962 / SU ML: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26438 1349 4.9 %RANDOM
Rwork0.2012 ---
all0.20423 26314 --
obs0.20423 26314 100 %-
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 mean: 25.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2--1.03 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.73→25.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6688 0 0 20 6708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0226870
X-RAY DIFFRACTIONr_bond_other_d0.0020.024568
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9519370
X-RAY DIFFRACTIONr_angle_other_deg1.093.00311184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1995864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06524.403268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.249151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9541522
X-RAY DIFFRACTIONr_chiral_restr0.1010.21052
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027600
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021346
X-RAY DIFFRACTIONr_nbd_refined0.2160.21118
X-RAY DIFFRACTIONr_nbd_other0.2130.24319
X-RAY DIFFRACTIONr_nbtor_refined0.1970.23264
X-RAY DIFFRACTIONr_nbtor_other0.1020.23910
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2143
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.26
X-RAY DIFFRACTIONr_mcbond_it0.9961.55341
X-RAY DIFFRACTIONr_mcbond_other0.21.51740
X-RAY DIFFRACTIONr_mcangle_it1.25127048
X-RAY DIFFRACTIONr_scbond_it1.83833058
X-RAY DIFFRACTIONr_scangle_it2.6684.52322
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1L2069tight positional0.060.05
2H2138tight positional0.050.05
1L761medium positional0.420.5
2H633medium positional0.360.5
1L2069tight thermal0.130.5
2H2138tight thermal0.110.5
1L761medium thermal0.532
2H633medium thermal0.462
LS refinement shellResolution: 2.732→2.802 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 84 -
Rwork0.371 1619 -
obs-1619 100 %

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