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- PDB-3bd4: Crystal structure of single domain VL of an anti-DNA binding anti... -

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Basic information

Entry
Database: PDB / ID: 3bd4
TitleCrystal structure of single domain VL of an anti-DNA binding antibody 3D8 scFv and its active site revealed by complex structures of a small molecule and metals
Componentscatalytic antibody
KeywordsIMMUNE SYSTEM / beta sandwich
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPark, S.K. / Kim, J.S.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of single-domain VL of an anti-DNA binding antibody 3D8 scFv and its active site revealed by complex structures of a small molecule and metals
Authors: Park, S.Y. / Lee, W.R. / Lee, S.C. / Kwon, M.H. / Kim, Y.S. / Kim, J.S.
History
DepositionNov 14, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 1.3Oct 30, 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: catalytic antibody
B: catalytic antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3545
Polymers24,9202
Non-polymers4343
Water1,820101
1
A: catalytic antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7823
Polymers12,4601
Non-polymers3222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: catalytic antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5722
Polymers12,4601
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-19.4 kcal/mol
Surface area10460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.852, 61.852, 92.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody catalytic antibody / DNA degrading antibody


Mass: 12460.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: 3d8 vl / Plasmid: pIg20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30 PEG 3350, 0.1M bis-tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.2 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 16, 2006 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 8425 / Num. obs: 8273 / % possible obs: 98.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.062
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5 % / Rsym value: 0.553 / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2GKI

2gki


Resolution: 2.4→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2811 827 -RANDOM
Rwork0.2128 ---
obs0.2128 7706 92.1 %-
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1708 0 16 101 1825
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_bond_d0.006
LS refinement shellResolution: 2.4→2.45 Å
RfactorNum. reflection
Rfree0.357 46
Rwork0.3214 -
obs-355

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