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- PDB-2gki: Heavy and light chain variable single domains of an anti-DNA bind... -

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Basic information

Entry
Database: PDB / ID: 2gki
TitleHeavy and light chain variable single domains of an anti-DNA binding antibody hydrolyze both double- and single-stranded DNAs without sequence specificity
Componentsnuclease
KeywordsIMMUNE SYSTEM / anti-DNA antibody / catalytic antibody
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region
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
: / : / Antigen, B-cell receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsKim, Y.R. / Kim, J.S. / Lee, S.H. / Lee, W.R. / Sohn, J.N. / Chung, Y.C. / Shim, H.K. / Lee, S.C. / Kwon, M.H. / Kim, Y.S.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Heavy and light chain variable single domains of an anti-DNA binding antibody hydrolyze both double- and single-stranded DNAs without sequence specificity.
Authors: Kim, Y.R. / Kim, J.S. / Lee, S.H. / Lee, W.R. / Sohn, J.N. / Chung, Y.C. / Shim, H.K. / Lee, S.C. / Kwon, M.H. / Kim, Y.S.
History
DepositionApr 2, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Oct 25, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Nov 20, 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
A: nuclease
B: nuclease


Theoretical massNumber of molelcules
Total (without water)63,0092
Polymers63,0092
Non-polymers00
Water1,26170
1
A: nuclease


Theoretical massNumber of molelcules
Total (without water)31,5041
Polymers31,5041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: nuclease


Theoretical massNumber of molelcules
Total (without water)31,5041
Polymers31,5041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: nuclease
B: nuclease

A: nuclease
B: nuclease


Theoretical massNumber of molelcules
Total (without water)126,0174
Polymers126,0174
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+11/61
Buried area8340 Å2
ΔGint-52 kcal/mol
Surface area42560 Å2
MethodPISA
4
A: nuclease

A: nuclease

B: nuclease

B: nuclease


Theoretical massNumber of molelcules
Total (without water)126,0174
Polymers126,0174
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_557x-y,-y,-z+21
crystal symmetry operation6_545x-y,x-1,z+1/61
crystal symmetry operation10_666-y+1,-x+1,-z+11/61
Buried area8020 Å2
ΔGint-45 kcal/mol
Surface area42880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.740, 179.740, 184.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Antibody nuclease


Mass: 31504.314 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pIg20 / Production host: Escherichia coli (E. coli)
References: GenBank: 8777863, GenBank: 8777865, UniProt: A0N274*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 6.814426 Å3/Da / Density % sol: 81.950058 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2M Lithium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 22, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.88→100 Å / Num. all: 40011 / Num. obs: 40011 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.8 % / Rmerge(I) obs: 0.078
Reflection shellResolution: 2.88→2.98 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCdata collection
DENZOdata reduction
PHASERphasing
CNS1.1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DZB

1dzb


Resolution: 2.88→49.58 Å / σ(F): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 4017 -RANDOM
Rwork0.212 ---
obs0.212 35975 99.4 %-
all-39992 --
Refinement stepCycle: LAST / Resolution: 2.88→49.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3684 0 0 70 3754

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