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

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Basic information

Entry
Database: PDB / ID: 4hii
TitleAnti-Streptococcus pneumoniae 23F Fab 023.102 with bound rhamnose-galactose
Components
  • Fab 023.102 heavy chain
  • Fab 023.102 light chain
KeywordsIMMUNE SYSTEM / Immunoglobin / Antibody / Streptococcus pneumoniae 23F
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 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 2.2Oct 16, 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 light chain
B: Fab 023.102 heavy chain
C: Fab 023.102 light chain
D: Fab 023.102 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4876
Polymers97,8354
Non-polymers6532
Water2,000111
1
A: Fab 023.102 light chain
B: Fab 023.102 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2443
Polymers48,9172
Non-polymers3261
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-22 kcal/mol
Surface area19330 Å2
MethodPISA
2
C: Fab 023.102 light chain
D: Fab 023.102 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2443
Polymers48,9172
Non-polymers3261
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-21 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.400, 66.900, 119.100
Angle α, β, γ (deg.)90.00, 111.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Fab 023.102 light chain


Mass: 23801.338 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 Fab 023.102 heavy chain


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: Polysaccharide alpha-L-rhamnopyranose-(1-2)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LRhapa1-2DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a2211m-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(2+1)][a-L-Rhap]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.73 Å3/Da / Density % sol: 54.91 %
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 16, 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: 2.3→17 Å / Num. all: 47340 / Num. obs: 44921 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.75 % / Rmerge(I) obs: 0.0395 / Net I/σ(I): 24.88
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 1.07 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 2.92 / Num. unique all: 2047 / % possible all: 67.6

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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: 2.3→17 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2190 -RANDOM
Rwork0.243 ---
all0.243 47005 --
obs0.243 43585 92.7 %-
Refinement stepCycle: LAST / Resolution: 2.3→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6293 0 44 111 6448
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005079
X-RAY DIFFRACTIONc_angle_deg1.59583

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