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- PDB-5xhg: Crystal structure of Trastuzumab Fab fragment bearing Ne-(o-azido... -

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Basic information

Entry
Database: PDB / ID: 5xhg
TitleCrystal structure of Trastuzumab Fab fragment bearing Ne-(o-azidobenzyloxycarbonyl)-L-lysine
Components
  • polypeptide(H)
  • polypeptide(L)
KeywordsIMMUNE SYSTEM / FAB
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / (2-azidophenyl)methyl hydrogen carbonate / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.76 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 1.1Sep 19, 2018Group: Data collection / Derived calculations ...Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_src_gen / pdbx_entity_nonpoly
Item: _chem_comp.formula_weight / _chem_comp.name ..._chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_entity_nonpoly.name
Revision 1.2Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,03719
Polymers93,7854
Non-polymers1,25215
Water22,6991260
1
A: polypeptide(L)
B: polypeptide(H)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4127
Polymers46,8922
Non-polymers5195
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-15 kcal/mol
Surface area19350 Å2
MethodPISA
2
C: polypeptide(L)
D: polypeptide(H)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,62512
Polymers46,8922
Non-polymers73310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-34 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.651, 79.891, 85.764
Angle α, β, γ (deg.)113.50, 92.82, 102.84
Int Tables number1
Space group name H-MP1

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Components

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody polypeptide(L)


Mass: 23467.082 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)


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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Non-polymers , 5 types, 1275 molecules

#3: Chemical ChemComp-OAZ / (2-azidophenyl)methyl hydrogen carbonate


Mass: 193.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7N3O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1260 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate, PEG 3350, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→30 Å / Num. obs: 230256 / % possible obs: 95.8 % / Redundancy: 1.3 % / Net I/σ(I): 7.92

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.76→25.438 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 20.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1994 1426 1.72 %
Rwork0.173 --
obs0.1735 83118 92.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→25.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6552 0 78 1260 7890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046820
X-RAY DIFFRACTIONf_angle_d0.8129279
X-RAY DIFFRACTIONf_dihedral_angle_d12.5952444
X-RAY DIFFRACTIONf_chiral_restr0.031037
X-RAY DIFFRACTIONf_plane_restr0.0041179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.82290.29331300.24747136X-RAY DIFFRACTION81
1.8229-1.89590.2591310.21877535X-RAY DIFFRACTION86
1.8959-1.98210.26071390.19657873X-RAY DIFFRACTION90
1.9821-2.08660.2131370.18748107X-RAY DIFFRACTION91
2.0866-2.21720.22051380.18238280X-RAY DIFFRACTION94
2.2172-2.38830.21241560.18358320X-RAY DIFFRACTION94
2.3883-2.62840.21891540.18388454X-RAY DIFFRACTION96
2.6284-3.00820.20481430.17638598X-RAY DIFFRACTION97
3.0082-3.78810.16391490.1528682X-RAY DIFFRACTION98
3.7881-25.44060.16551490.14918707X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 21.188 Å / Origin y: 63.57 Å / Origin z: 7.8992 Å
111213212223313233
T0.0187 Å20.0046 Å20.0049 Å2-0.0398 Å20.0046 Å2--0.051 Å2
L0.2597 °20.0269 °20.0522 °2-0.2687 °2-0.0836 °2--0.2655 °2
S0.0242 Å °-0.0326 Å °-0.0222 Å °-0.0103 Å °-0.0134 Å °0.0121 Å °-0.0103 Å °0.0045 Å °-0.0026 Å °
Refinement TLS groupSelection details: all

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