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- PDB-5i0z: Crystal structure of the single domain catalytic antibody 3D8-VH -

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Basic information

Entry
Database: PDB / ID: 5i0z
TitleCrystal structure of the single domain catalytic antibody 3D8-VH
Componentscatalytic DNA antibody
KeywordsIMMUNE SYSTEM / 3D8 scFv / 3D8-VH
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPark, S.Y. / Kim, J.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Chonnam National University2015-0597 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of the single domain catalytic antibody 3D8-VH
Authors: Park, S.Y. / Kim, B.N.
History
DepositionFeb 4, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 15, 2017Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.3Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 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 DNA antibody
B: catalytic DNA antibody


Theoretical massNumber of molelcules
Total (without water)31,6302
Polymers31,6302
Non-polymers00
Water6,305350
1
A: catalytic DNA antibody


Theoretical massNumber of molelcules
Total (without water)15,8151
Polymers15,8151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: catalytic DNA antibody


Theoretical massNumber of molelcules
Total (without water)15,8151
Polymers15,8151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.775, 85.820, 50.202
Angle α, β, γ (deg.)90.00, 100.87, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-309-

HOH

21B-351-

HOH

31B-352-

HOH

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Components

#1: Antibody catalytic DNA antibody


Mass: 15814.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 1.97 Å3/Da / Density % sol: 37.42 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 30 % (w/v) PEG 8000 and 0.1 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.24 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 16712 / % possible obs: 96.3 % / Redundancy: 2.7 % / Net I/σ(I): 6.3
Reflection shellResolution: 1.9→2 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GKI

2gki


Resolution: 1.9→37.402 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.27
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2622 1700 4.95 %
Rwork0.2176 --
obs0.2198 16712 90.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→37.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1860 0 0 350 2210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041931
X-RAY DIFFRACTIONf_angle_d0.982609
X-RAY DIFFRACTIONf_dihedral_angle_d13.887697
X-RAY DIFFRACTIONf_chiral_restr0.078269
X-RAY DIFFRACTIONf_plane_restr0.005328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95590.34391430.28972790X-RAY DIFFRACTION93
1.9559-2.0190.32481500.27462771X-RAY DIFFRACTION93
2.019-2.09120.29981510.26292805X-RAY DIFFRACTION92
2.0912-2.17490.25491480.25552785X-RAY DIFFRACTION92
2.1749-2.27390.3121390.23462751X-RAY DIFFRACTION92
2.2739-2.39370.2881400.24352702X-RAY DIFFRACTION91
2.3937-2.54370.31531470.22812733X-RAY DIFFRACTION91
2.5437-2.740.27641420.23242745X-RAY DIFFRACTION90
2.74-3.01570.23631380.21242677X-RAY DIFFRACTION90
3.0157-3.45180.26981400.19572686X-RAY DIFFRACTION89
3.4518-4.34780.19661310.17442620X-RAY DIFFRACTION87
4.3478-37.40930.22991310.19192568X-RAY DIFFRACTION85
Refinement TLS params.Method: refined / Origin x: -16.2106 Å / Origin y: 3.1102 Å / Origin z: -0.0331 Å
111213212223313233
T0.0825 Å20.0007 Å20.008 Å2-0.0865 Å20.017 Å2--0.12 Å2
L0.451 °20.0552 °2-0.1775 °2-0.6604 °20.514 °2--1.7124 °2
S0.0139 Å °-0.023 Å °0.002 Å °-0.0002 Å °-0.0393 Å °-0.0114 Å °0.0147 Å °0.0862 Å °0.023 Å °
Refinement TLS groupSelection details: all

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