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- PDB-2eh7: Crystal structure of humanized KR127 FAB -

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Basic information

Entry
Database: PDB / ID: 2eh7
TitleCrystal structure of humanized KR127 FAB
Components
  • HUMANIZED KR127 FAB, HEAVY CHAIN
  • HUMANIZED KR127 FAB, LIGHT CHAIN
KeywordsIMMUNE SYSTEM / HEPATITIS B VIRUS / HUMANIZED ANTIBODY / MONOCLONAL ANTIBODY / NEUTRALIZATION / PRES1
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChi, S.-W. / Kim, S.-J. / Maeng, C.-Y. / Hong, H.J. / Ryu, S.-E.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Broadly neutralizing anti-hepatitis B virus antibody reveals a complementarity determining region H3 lid-opening mechanism
Authors: Chi, S.-W. / Maeng, C.-Y. / Kim, S.J. / Oh, M.S. / Ryu, C.J. / Kim, S.-J. / Han, K.-H. / Hong, H.J. / Ryu, S.-E.
History
DepositionMar 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Oct 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: HUMANIZED KR127 FAB, LIGHT CHAIN
H: HUMANIZED KR127 FAB, HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)46,9782
Polymers46,9782
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-24 kcal/mol
Surface area19330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.120, 61.110, 77.530
Angle α, β, γ (deg.)90.00, 91.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody HUMANIZED KR127 FAB, LIGHT CHAIN


Mass: 23891.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: HUMANIZED KR127 / Plasmid: PCMV / Cell (production host): DHFR-DEFICIENT CHO CELL / Cell line (production host): DG44 / Production host: Homo sapiens (human)
#2: Antibody HUMANIZED KR127 FAB, HEAVY CHAIN


Mass: 23086.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: HUMANIZED KR127 / Plasmid: PCMV / Cell (production host): DHFR-DEFICIENT CHO CELL / Cell line (production host): DG44 / Production host: Homo sapiens (human)
Has protein modificationY
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THE SEQUENCES ARE SHOWN IN ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THE SEQUENCES ARE SHOWN IN THE PAPER(FIGURE 1): HONG, H.J. ET AL., VIROLOGY 318, 134-141 (2004)

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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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17% PEG 4000, 10mM Hepes-NaOH, 0.2M ammonium sulfate, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 9, 2001
RadiationMonochromator: CONFOCAL MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→31.31 Å / Num. all: 16404 / Num. obs: 15758 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.078 / Net I/σ(I): 5.9
Reflection shellResolution: 2.5→2.66 Å / % possible all: 97.5

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AJ7

1aj7


Resolution: 2.5→31.31 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.252 773 -RANDOM
Rwork0.207 ---
obs0.207 15758 100 %-
all-16404 --
Refinement stepCycle: LAST / Resolution: 2.5→31.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3302 0 0 0 3302
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_dihedral_angle_d26.72
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.5→2.66 Å / % reflection obs: 97.5 %

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