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- PDB-4hih: Anti-Streptococcus pneumoniae 23F Fab 023.102 with bound rhamnose. -

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Basic information

Entry
Database: PDB / ID: 4hih
TitleAnti-Streptococcus pneumoniae 23F Fab 023.102 with bound rhamnose.
Components
  • Antibody 023.102
  • Fab 023.102
KeywordsIMMUNE SYSTEM / Immunoglobin / Antibody / Streptococcus pneumoniae 23F
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / alpha-L-rhamnopyranose
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBryson, S. / Risnes, L. / Damgupta, S. / Thomson, C.A. / 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
DepositionOct 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _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
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 27, 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
A: Fab 023.102
B: Antibody 023.102
C: Fab 023.102
D: Antibody 023.102
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4196
Polymers98,0914
Non-polymers3282
Water5,621312
1
A: Fab 023.102
B: Antibody 023.102
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2103
Polymers49,0462
Non-polymers1641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-20 kcal/mol
Surface area18640 Å2
MethodPISA
2
C: Fab 023.102
D: Antibody 023.102
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2103
Polymers49,0462
Non-polymers1641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-20 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.790, 66.680, 109.280
Angle α, β, γ (deg.)90.00, 101.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab 023.102


Mass: 23929.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pARC / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue
#2: Antibody Antibody 023.102


Mass: 25116.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pARC / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue
#3: 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.: 2
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.05M Na Citrate, pH 3-4, 18% PEG 3350, 0.2M Li Acetate , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 18, 2010 / Details: Rigaku Osmic VariMax
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→17 Å / Num. all: 70705 / Num. obs: 69510 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.81 % / Rmerge(I) obs: 0.0527 / Net I/σ(I): 17.86
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.43 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2.94 / Num. unique all: 4326 / % possible all: 86.6

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Processing

Software
NameClassification
MAR345dtbdata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HIE

4hie


Resolution: 2→17 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.236 3360 RANDOM
Rwork0.224 --
all0.224 70413 -
obs0.224 67221 -
Refinement stepCycle: LAST / Resolution: 2→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6318 0 22 312 6652
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006117
X-RAY DIFFRACTIONc_angle_deg1.58193

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