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- PDB-6bjz: Crystal Structure of the Fab fragment of humanized 5c8 antibody c... -

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Basic information

Entry
Database: PDB / ID: 6bjz
TitleCrystal Structure of the Fab fragment of humanized 5c8 antibody containing the fluorescent non-canonical amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine at pH 5.5
Components
  • 5c8 Fab Heavy chain
  • 5c8 Fab Light chain
KeywordsIMMUNE SYSTEM / Immunoglobulin / Non Canonical Aminoacid
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsHenderson, J.N. / Simmons, C.R. / Mills, J.H.
CitationJournal: Biochemistry / Year: 2020
Title: Structural Insights into How Protein Environments Tune the Spectroscopic Properties of a Noncanonical Amino Acid Fluorophore.
Authors: Henderson, J.N. / Simmons, C.R. / Fahmi, N.E. / Jeffs, J.W. / Borges, C.R. / Mills, J.H.
History
DepositionNov 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
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
Revision 1.2Oct 4, 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 1.3Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 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
H: 5c8 Fab Heavy chain
L: 5c8 Fab Light chain


Theoretical massNumber of molelcules
Total (without water)48,0922
Polymers48,0922
Non-polymers00
Water9,458525
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-23 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.813, 59.911, 73.459
Angle α, β, γ (deg.)90.000, 96.480, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-305-

HOH

21H-520-

HOH

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Components

#1: Antibody 5c8 Fab Heavy chain


Mass: 24078.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pBLN200 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10
#2: Antibody 5c8 Fab Light chain


Mass: 24013.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pBLN200 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.05 Å3/Da / Density % sol: 40.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.3
Details: 27% PEG 3350, 0.1 M Citric Acid/Sodium Citrate pH 3.3
PH range: 3-4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00003 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.45→72.99 Å / Num. obs: 69300 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.031 / Rrim(I) all: 0.086 / Χ2: 0.875 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.45-1.486.10.73234530.7870.3220.8020.47
1.48-1.56.70.7134770.8110.2960.770.485
1.5-1.537.10.62334170.870.2520.6730.521
1.53-1.567.30.52834500.9080.2110.5690.527
1.56-1.67.40.45934930.9310.1820.4940.539
1.6-1.637.40.40134040.9440.1590.4320.554
1.63-1.677.40.34434350.9610.1360.3710.568
1.67-1.727.40.27434550.9690.1080.2950.6
1.72-1.777.40.22134490.980.0870.2380.648
1.77-1.837.40.17934710.9860.070.1920.728
1.83-1.897.40.14834510.990.0580.1590.84
1.89-1.977.50.1234470.9930.0470.1291.053
1.97-2.067.40.10134780.9940.040.1091.228
2.06-2.177.50.09534660.9950.0370.1021.322
2.17-2.37.50.08934490.9950.0350.0961.495
2.3-2.487.50.08434690.9950.0330.091.148
2.48-2.737.40.07234950.9960.0280.0781.12
2.73-3.127.30.05934680.9970.0230.0631.23
3.12-3.947.50.04635060.9980.0180.0491.14
3.94-507.50.03735670.9990.0150.041.093

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.45 Å49.91 Å
Translation6.67 Å49.91 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.5.6phasing
REFMACrefinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I9R

1i9r


Resolution: 1.45→72.99 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.396 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0647 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.061
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1699 3416 4.9 %RANDOM
Rwork0.1216 ---
obs0.124 65883 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 51.14 Å2 / Biso mean: 16.244 Å2 / Biso min: 4.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.04 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.45→72.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3303 0 0 525 3828
Biso mean---27.97 -
Num. residues----440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023535
X-RAY DIFFRACTIONr_bond_other_d0.0020.023180
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.9544864
X-RAY DIFFRACTIONr_angle_other_deg1.0033.0037409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1635492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47125.308130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3215556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.539157
X-RAY DIFFRACTIONr_chiral_restr0.1130.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214093
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02765
X-RAY DIFFRACTIONr_rigid_bond_restr2.72336713
X-RAY DIFFRACTIONr_sphericity_free21.5615141
X-RAY DIFFRACTIONr_sphericity_bonded7.53556986
LS refinement shellResolution: 1.451→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 251 -
Rwork0.196 4788 -
all-5039 -
obs--98.51 %

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