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- PDB-4ptu: Crystal Structure of anti-23F strep Fab C05 with rhamnose -

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Basic information

Entry
Database: PDB / ID: 4ptu
TitleCrystal Structure of anti-23F strep Fab C05 with rhamnose
Components
  • Antibody pn132p2C05, heavy chain
  • Antibody pn132p2C05, light chain
KeywordsIMMUNE SYSTEM / Antibody / Fab fragment / 23F / Rhamnose
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION / alpha-L-rhamnopyranose
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.511 Å
AuthorsBryson, S. / Risnes, L. / Damgupta, S. / Thomson, C.A. / Smith, K. / Schrader, J.W. / Pai, E.F.
CitationJournal: J. Immunol. / Year: 2016
Title: Structures of Preferred Human IgV Genes-Based Protective Antibodies Identify How Conserved Residues Contact Diverse Antigens and Assign Source of Specificity to CDR3 Loop Variation.
Authors: Bryson, S. / Thomson, C.A. / Risnes, L.F. / Dasgupta, S. / Smith, K. / Schrader, J.W. / Pai, E.F.
History
DepositionMar 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antibody pn132p2C05, light chain
B: Antibody pn132p2C05, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5455
Polymers48,2632
Non-polymers2823
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-28 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.150, 48.740, 79.310
Angle α, β, γ (deg.)90.00, 120.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Antibody pn132p2C05, light chain


Mass: 23534.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle
#2: Antibody Antibody pn132p2C05, heavy chain


Mass: 24728.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Sugar ChemComp-RAM / alpha-L-rhamnopyranose / alpha-L-rhamnose / 6-deoxy-alpha-L-mannopyranose / L-rhamnose / rhamnose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LRhapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-rhamnopyranoseCOMMON NAMEGMML 1.0
a-L-RhapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RhaSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M Na Acetate, 20% PEG 1500, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.51→41.5 Å / Num. all: 68557 / Num. obs: 68342 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rsym value: 0.0322 / Net I/σ(I): 29.22
Reflection shellResolution: 1.51→1.55 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 6.12 / Num. unique all: 4807 / Rsym value: 0.147 / % possible all: 97.4

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Processing

Software
NameVersionClassification
GM/CAJBluIce-EPICSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4HIE

4hie


Resolution: 1.511→41.454 Å / SU ML: 0.13 / σ(F): 0 / Phase error: 20.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 3386 4.99 %Random
Rwork0.179 ---
obs0.1803 67826 98.92 %-
all-68567 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.511→41.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3230 0 19 350 3599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073374
X-RAY DIFFRACTIONf_angle_d1.1574599
X-RAY DIFFRACTIONf_dihedral_angle_d13.0421207
X-RAY DIFFRACTIONf_chiral_restr0.046522
X-RAY DIFFRACTIONf_plane_restr0.005595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5112-1.53280.20611230.19582508X-RAY DIFFRACTION93
1.5328-1.55570.20971240.19182657X-RAY DIFFRACTION98
1.5557-1.580.21831410.18632627X-RAY DIFFRACTION98
1.58-1.60590.22011320.19372644X-RAY DIFFRACTION98
1.6059-1.63360.26781590.19062617X-RAY DIFFRACTION98
1.6336-1.66330.25281310.19112649X-RAY DIFFRACTION98
1.6633-1.69530.19291370.18442685X-RAY DIFFRACTION99
1.6953-1.72990.23331440.18882662X-RAY DIFFRACTION99
1.7299-1.76750.23291280.18722691X-RAY DIFFRACTION99
1.7675-1.80860.22211400.18512687X-RAY DIFFRACTION99
1.8086-1.85380.24591430.18052679X-RAY DIFFRACTION100
1.8538-1.90390.20161530.1882680X-RAY DIFFRACTION100
1.9039-1.960.2331490.19122693X-RAY DIFFRACTION100
1.96-2.02320.25741550.18252695X-RAY DIFFRACTION100
2.0232-2.09550.20431270.18832711X-RAY DIFFRACTION100
2.0955-2.17940.20731600.17852663X-RAY DIFFRACTION100
2.1794-2.27860.22671350.18752735X-RAY DIFFRACTION100
2.2786-2.39870.21721380.19422716X-RAY DIFFRACTION100
2.3987-2.5490.26881500.18862706X-RAY DIFFRACTION100
2.549-2.74580.25051140.19752757X-RAY DIFFRACTION100
2.7458-3.0220.19351450.19652716X-RAY DIFFRACTION100
3.022-3.45910.2011630.182741X-RAY DIFFRACTION100
3.4591-4.35740.16041310.15372755X-RAY DIFFRACTION100
4.3574-41.46920.15771640.15192766X-RAY DIFFRACTION98

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