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- PDB-7rki: Griffithsin-S10Y/S42Y/S88Y -

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Basic information

Entry
Database: PDB / ID: 7rki
TitleGriffithsin-S10Y/S42Y/S88Y
ComponentsGriffithsin
KeywordsSUGAR BINDING PROTEIN / complex
Function / homology
Function and homology information


N-acetylgalactosamine binding / D-glucose binding / D-mannose binding / carbohydrate binding / identical protein binding
Similarity search - Function
Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily
Similarity search - Domain/homology
alpha-D-mannopyranose / Griffithsin
Similarity search - Component
Biological speciesGriffithsia sp. (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsSun, J.D. / Zhao, G.X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)1ZIADK032103-21 United States
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: C 3 -Symmetric Aromatic Core of Griffithsin Is Essential for Potent Anti-HIV Activity.
Authors: Sun, J. / Zhao, G. / Bylund, T. / Lee, M. / Adibhatla, S. / Kwong, P.D. / Chuang, G.Y. / Rawi, R. / Bewley, C.A.
History
DepositionJul 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: 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
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Griffithsin
B: Griffithsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6335
Polymers30,0932
Non-polymers5403
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-12 kcal/mol
Surface area10090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.745, 59.655, 67.288
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Griffithsin / GRFT


Mass: 15046.390 Da / Num. of mol.: 2 / Mutation: S10Y, S42Y, S88Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Griffithsia sp. (strain Q66D336) (eukaryote)
Strain: Q66D336 / Production host: Escherichia coli (E. coli) / References: UniProt: P84801
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.93 Å3/Da / Density % sol: 36.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M citric acid, pH 3.1, 2.6 M sodium chloride

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.09→25 Å / Num. obs: 13650 / % possible obs: 96.3 % / Redundancy: 7 % / Biso Wilson estimate: 23.22 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.9
Reflection shellResolution: 2.09→2.14 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.067 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1368 / % possible all: 88.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.17.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GUC

2guc


Resolution: 2.09→21.91 Å / SU ML: 0.235 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.6737
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2286 1368 10.04 %
Rwork0.1727 12252 -
obs0.1784 13620 95.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.29 Å2
Refinement stepCycle: LAST / Resolution: 2.09→21.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1824 0 36 124 1984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641912
X-RAY DIFFRACTIONf_angle_d0.87512587
X-RAY DIFFRACTIONf_chiral_restr0.0548269
X-RAY DIFFRACTIONf_plane_restr0.004338
X-RAY DIFFRACTIONf_dihedral_angle_d7.0793311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.170.28451110.20771061X-RAY DIFFRACTION84.5
2.17-2.250.26231380.18251199X-RAY DIFFRACTION95.3
2.25-2.360.30721350.19261199X-RAY DIFFRACTION95.56
2.36-2.480.2511330.20831212X-RAY DIFFRACTION96
2.48-2.640.26611360.20191208X-RAY DIFFRACTION96.55
2.64-2.840.30091360.19391234X-RAY DIFFRACTION96.82
2.84-3.120.23781430.18761230X-RAY DIFFRACTION97.38
3.12-3.570.22431410.15541262X-RAY DIFFRACTION97.7
3.58-4.50.18611420.14241287X-RAY DIFFRACTION98.62
4.5-21.910.17431530.1591360X-RAY DIFFRACTION99.28

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