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- PDB-6b3k: Crystal structure of mutant Spinach RNA aptamer in complex with F... -

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Basic information

Entry
Database: PDB / ID: 6b3k
TitleCrystal structure of mutant Spinach RNA aptamer in complex with Fab BL3-6
Components
  • Heavy chain of Fab BL3-6
  • Light chain of Fab BL3-6
  • RNA (83-MER),RNA (83-MER)
Keywordsimmune system/rna / RNA aptamer / Fragment of antibody / Chaperone-assisted RNA Crystallography / immune system-rna complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / RNA / RNA (> 10)
Function and homology information
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsDasGupta, S. / Koirala, D. / Shelke, S.A. / Piccirilli, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI081987 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM102489 United States
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Affinity maturation of a portable Fab-RNA module for chaperone-assisted RNA crystallography.
Authors: Koirala, D. / Shelke, S.A. / Dupont, M. / Ruiz, S. / DasGupta, S. / Bailey, L.J. / Benner, S.A. / Piccirilli, J.A.
History
DepositionSep 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_audit_support / struct / struct_keywords
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _entity.pdbx_description / _pdbx_audit_support.funding_organization / _struct.title / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 13, 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: Heavy chain of Fab BL3-6
L: Light chain of Fab BL3-6
R: RNA (83-MER),RNA (83-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2054
Polymers74,1813
Non-polymers241
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-39 kcal/mol
Surface area33040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.216, 80.019, 93.405
Angle α, β, γ (deg.)90.00, 111.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Heavy chain of Fab BL3-6


Mass: 23852.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody Light chain of Fab BL3-6


Mass: 23394.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: RNA chain RNA (83-MER),RNA (83-MER)


Mass: 26933.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 3.45 Å3/Da / Density % sol: 64.36 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 8% Tacsimate (pH 7.0), 20% Polyethylene glycol 3,350, 0.1 M HEPES (pH 7.2)

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 11, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.09→69.1 Å / Num. obs: 58291 / % possible obs: 97.6 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Net I/σ(I): 12.3
Reflection shellResolution: 2.09→2.165 Å / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.996 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KZE

4kze


Resolution: 2.09→69.097 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.67
RfactorNum. reflection% reflection
Rfree0.2258 2000 3.43 %
Rwork0.1926 --
obs0.1938 58275 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.09→69.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 1786 1 256 5364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075401
X-RAY DIFFRACTIONf_angle_d0.8847744
X-RAY DIFFRACTIONf_dihedral_angle_d9.1763020
X-RAY DIFFRACTIONf_chiral_restr0.048933
X-RAY DIFFRACTIONf_plane_restr0.006673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.14230.31221410.29153990X-RAY DIFFRACTION97
2.1423-2.20020.29331440.26834020X-RAY DIFFRACTION98
2.2002-2.2650.28071420.2634010X-RAY DIFFRACTION98
2.265-2.33810.2461430.25043997X-RAY DIFFRACTION97
2.3381-2.42170.30351410.24343994X-RAY DIFFRACTION97
2.4217-2.51860.2891390.24893895X-RAY DIFFRACTION94
2.5186-2.63320.26611420.23293996X-RAY DIFFRACTION98
2.6332-2.77210.24851450.23414064X-RAY DIFFRACTION98
2.7721-2.94580.27821430.21854054X-RAY DIFFRACTION98
2.9458-3.17320.23091440.21064034X-RAY DIFFRACTION98
3.1732-3.49250.22481410.18663990X-RAY DIFFRACTION96
3.4925-3.99790.22421460.17274093X-RAY DIFFRACTION99
3.9979-5.03670.1891430.14954009X-RAY DIFFRACTION97
5.0367-69.13470.1831460.16754129X-RAY DIFFRACTION97

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