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- PDB-6lun: NN2101 Antibody Fab fragment -

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Basic information

Entry
Database: PDB / ID: 6lun
TitleNN2101 Antibody Fab fragment
Components(NN2101) x 2
KeywordsSTRUCTURAL PROTEIN / Antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKim, H.N. / Seo, M.D. / Park, S.K.
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Development and characterization of a fully human antibody targeting SCF/c-kit signaling.
Authors: Kim, J.O. / Kim, H.N. / Kim, K.H. / Baek, E.J. / Park, J.Y. / Ha, K. / Heo, D.R. / Seo, M.D. / Park, S.G.
History
DepositionJan 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NN2101
B: NN2101
C: NN2101
D: NN2101


Theoretical massNumber of molelcules
Total (without water)94,6784
Polymers94,6784
Non-polymers00
Water21,9961221
1
A: NN2101
B: NN2101


Theoretical massNumber of molelcules
Total (without water)47,3392
Polymers47,3392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-25 kcal/mol
Surface area18760 Å2
MethodPISA
2
C: NN2101
D: NN2101


Theoretical massNumber of molelcules
Total (without water)47,3392
Polymers47,3392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-24 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.753, 69.702, 90.058
Angle α, β, γ (deg.)90.00, 107.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody NN2101


Mass: 23477.213 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody NN2101


Mass: 23861.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1221 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) PEG 6000, 100mM HEPES-NaOH pH7.0, 200mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.9→36.531 Å / Num. obs: 66823 / % possible obs: 97.02 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.047 / Net I/σ(I): 26
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 3291 / CC1/2: 0.993

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data collection
PHENIXphasing
PHENIXmodel building
HKL-2000data scaling
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5bvp

5bvp


Resolution: 1.9→36.531 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.67
RfactorNum. reflection% reflection
Rfree0.2098 1968 3.01 %
Rwork0.1653 --
obs0.1667 65444 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→36.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6316 0 0 1221 7537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076469
X-RAY DIFFRACTIONf_angle_d0.8688809
X-RAY DIFFRACTIONf_dihedral_angle_d12.3163848
X-RAY DIFFRACTIONf_chiral_restr0.056986
X-RAY DIFFRACTIONf_plane_restr0.0051132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.26651300.19134165X-RAY DIFFRACTION90
1.9475-2.00010.24711340.18014345X-RAY DIFFRACTION93
2.0001-2.0590.21191360.17224376X-RAY DIFFRACTION94
2.059-2.12540.28581360.17194452X-RAY DIFFRACTION95
2.1254-2.20140.22281400.16614487X-RAY DIFFRACTION96
2.2014-2.28950.24131420.16594510X-RAY DIFFRACTION97
2.2895-2.39370.20831410.16864547X-RAY DIFFRACTION97
2.3937-2.51990.22261410.17284563X-RAY DIFFRACTION97
2.5199-2.67770.221420.18434583X-RAY DIFFRACTION98
2.6777-2.88440.26011430.18274639X-RAY DIFFRACTION98
2.8844-3.17450.22221450.17284650X-RAY DIFFRACTION99
3.1745-3.63350.1891440.15164677X-RAY DIFFRACTION99
3.6335-4.57640.16161460.13494724X-RAY DIFFRACTION100
4.5764-36.5310.17151480.16694758X-RAY DIFFRACTION99

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