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- PDB-7rid: Griffithsin variant Y28A -

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Basic information

Entry
Database: PDB / ID: 7rid
TitleGriffithsin variant Y28A
ComponentsGriffithsin
KeywordsSUGAR BINDING PROTEIN / complex / mannose binding protein
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
Biological speciesGriffithsia sp. (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhao, G. / Sun, J. / Bewley, C.A.
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 19, 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


Theoretical massNumber of molelcules
Total (without water)14,7261
Polymers14,7261
Non-polymers00
Water905
1
A: Griffithsin

A: Griffithsin


Theoretical massNumber of molelcules
Total (without water)29,4522
Polymers29,4522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area2040 Å2
ΔGint-8 kcal/mol
Surface area9940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.113, 79.113, 119.814
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-203-

HOH

21A-205-

HOH

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Components

#1: Protein Griffithsin / GRFT


Mass: 14726.003 Da / Num. of mol.: 1 / Mutation: Y28A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 3.68 Å3/Da / Density % sol: 66.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M bis-tris, pH 6.5 0.2 M calcium chloride dihydrate 45% v/v (+/-)-2-methyl-2,4-pentanediol

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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 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 10413 / % possible obs: 99.9 % / Redundancy: 18.2 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 30.5
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 8.1 / Num. unique obs: 511

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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: 2.3→25.31 Å / Cross valid method: FREE R-VALUE / σ(F): 100 / Phase error: 12.3684
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1639 1039 10 %
Rwork0.1523 9351 -
obs0.1604 10390 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 7.21 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms813 0 0 5 818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037829
X-RAY DIFFRACTIONf_angle_d0.71961120
X-RAY DIFFRACTIONf_chiral_restr0.0537117
X-RAY DIFFRACTIONf_plane_restr0.0038151
X-RAY DIFFRACTIONf_dihedral_angle_d7.0903122
LS refinement shellResolution: 2.3→2.34 Å
RfactorNum. reflection% reflection
Rfree0.1741 162 -
Rwork0.174 1453 -
obs--89.97 %

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