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- PDB-5h2b: Structure of a novel antibody G196 -

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Basic information

Entry
Database: PDB / ID: 5h2b
TitleStructure of a novel antibody G196
Components
  • G196 antibody Heavy chain
  • G196 antibody Light chain
KeywordsIMMUNE SYSTEM / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.001 Å
AuthorsPark, S.Y. / Sugiyama, K.
CitationJournal: Sci Rep / Year: 2017
Title: G196 epitope tag system: a novel monoclonal antibody, G196, recognizes the small, soluble peptide DLVPR with high affinity.
Authors: Tatsumi, K. / Sakashita, G. / Nariai, Y. / Okazaki, K. / Kato, H. / Obayashi, E. / Yoshida, H. / Sugiyama, K. / Park, S.Y. / Sekine, J. / Urano, T.
History
DepositionOct 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Structure summary
Revision 1.2Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: G196 antibody Heavy chain
B: G196 antibody Light chain


Theoretical massNumber of molelcules
Total (without water)47,2642
Polymers47,2642
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-21 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.647, 82.267, 127.312
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody G196 antibody Heavy chain


Mass: 23601.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody G196 antibody Light chain


Mass: 23662.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 293.2 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M sodium citrate, 20% PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 26685 / % possible obs: 94.3 % / Redundancy: 5.1 % / Net I/σ(I): 18.7

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Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementResolution: 2.001→41.134 Å / SU ML: 0.66 / Cross valid method: NONE / σ(F): 1.51 / Phase error: 29.21
RfactorNum. reflection% reflection
Rfree0.2807 1345 5.05 %
Rwork0.2112 --
obs0.2147 26648 94.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 40.655 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.1808 Å20 Å2-0 Å2
2--4.0933 Å20 Å2
3----7.1394 Å2
Refinement stepCycle: LAST / Resolution: 2.001→41.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 0 108 3386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083367
X-RAY DIFFRACTIONf_angle_d1.1444583
X-RAY DIFFRACTIONf_dihedral_angle_d17.551197
X-RAY DIFFRACTIONf_chiral_restr0.085513
X-RAY DIFFRACTIONf_plane_restr0.006580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0006-2.07210.36251040.30472261X-RAY DIFFRACTION86
2.0721-2.1550.3611330.29282363X-RAY DIFFRACTION89
2.155-2.25310.34841390.26552384X-RAY DIFFRACTION92
2.2531-2.37190.30711460.24542447X-RAY DIFFRACTION93
2.3719-2.52050.3191380.24452501X-RAY DIFFRACTION94
2.5205-2.7150.34781090.23912565X-RAY DIFFRACTION96
2.715-2.98820.32181360.23162591X-RAY DIFFRACTION96
2.9882-3.42040.2881620.21572639X-RAY DIFFRACTION99
3.4204-4.30860.24911400.19012717X-RAY DIFFRACTION99
4.3086-41.14220.22131380.16432835X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 17.6382 Å / Origin y: 17.7983 Å / Origin z: 29.3473 Å
111213212223313233
T0.1486 Å2-0.0502 Å20.0318 Å2-0.1982 Å2-0.0185 Å2--0.1476 Å2
L-0.0058 °2-0.3696 °2-0.176 °2-1.3017 °2-0.2623 °2--2.4591 °2
S0.0634 Å °-0.0559 Å °-0.0502 Å °0.2538 Å °-0.0173 Å °0.0584 Å °-0.1623 Å °-0.0823 Å °-0.0224 Å °
Refinement TLS groupSelection details: all

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