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- PDB-5xhf: Crystal structure of Trastuzumab Fab fragment bearing p-azido-L-p... -

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Basic information

Entry
Database: PDB / ID: 5xhf
TitleCrystal structure of Trastuzumab Fab fragment bearing p-azido-L-phenylalanine
Components
  • polypeptide (H chain)
  • polypeptide (L chain)
KeywordsIMMUNE SYSTEM / FAB
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.205 Å
AuthorsKuratani, M. / Yanagisawa, T. / Sakamoto, K. / Yokoyama, S.
CitationJournal: Bioconjug. Chem. / Year: 2017
Title: Extensive Survey of Antibody Invariant Positions for Efficient Chemical Conjugation Using Expanded Genetic Codes.
Authors: Kato, A. / Kuratani, M. / Yanagisawa, T. / Ohtake, K. / Hayashi, A. / Amano, Y. / Kimura, K. / Yokoyama, S. / Sakamoto, K. / Shiraishi, Y.
History
DepositionApr 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_description ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_description / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: polypeptide (L chain)
B: polypeptide (H chain)
C: polypeptide (L chain)
D: polypeptide (H chain)


Theoretical massNumber of molelcules
Total (without water)93,9054
Polymers93,9054
Non-polymers00
Water0
1
A: polypeptide (L chain)
B: polypeptide (H chain)


Theoretical massNumber of molelcules
Total (without water)46,9522
Polymers46,9522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-22 kcal/mol
Surface area19330 Å2
MethodPISA
2
C: polypeptide (L chain)
D: polypeptide (H chain)


Theoretical massNumber of molelcules
Total (without water)46,9522
Polymers46,9522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-26 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.841, 80.067, 85.792
Angle α, β, γ (deg.)113.67, 92.35, 102.78
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody polypeptide (L chain)


Mass: 23527.096 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Description: humanized mouse
Production host: Escherichia coli str. K-12 substr. W3110 (bacteria)
#2: Antibody polypeptide (H chain)


Mass: 23425.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Description: humanized mouse
Production host: Escherichia coli str. K-12 substr. W3110 (bacteria)

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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: 2.51 Å3/Da / Density % sol: 51.01 % / Description: THE FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 20000, MES-Na

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Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 14758 / % possible obs: 95.7 % / Redundancy: 1.3 % / Net I/σ(I): 2.45

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N8Z

1n8z


Resolution: 3.205→42.443 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 32.76 / Details: THE FILE CONTAINS FRIEDEL PAIRS.
RfactorNum. reflection% reflection
Rfree0.2966 1473 9.98 %
Rwork0.2194 --
obs0.227 14758 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.205→42.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6562 0 0 0 6562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026747
X-RAY DIFFRACTIONf_angle_d0.4829199
X-RAY DIFFRACTIONf_dihedral_angle_d10.3824016
X-RAY DIFFRACTIONf_chiral_restr0.0411032
X-RAY DIFFRACTIONf_plane_restr0.0041174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2051-3.30850.34781410.28571182X-RAY DIFFRACTION97
3.3085-3.42670.29491240.24881210X-RAY DIFFRACTION98
3.4267-3.56380.34731360.24731219X-RAY DIFFRACTION98
3.5638-3.72590.3381330.24361182X-RAY DIFFRACTION98
3.7259-3.92220.30881340.24221227X-RAY DIFFRACTION98
3.9222-4.16770.30751280.22091197X-RAY DIFFRACTION98
4.1677-4.48920.31691390.19441218X-RAY DIFFRACTION98
4.4892-4.94040.25831330.1921210X-RAY DIFFRACTION98
4.9404-5.65380.29251370.19641213X-RAY DIFFRACTION99
5.6538-7.11780.25331350.21741198X-RAY DIFFRACTION99
7.1178-42.44620.24421330.19651229X-RAY DIFFRACTION99

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