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- PDB-7ric: Griffithsin variant Y28W/Y68W/Y110W -

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Basic information

Entry
Database: PDB / ID: 7ric
TitleGriffithsin variant Y28W/Y68W/Y110W
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
Biological speciesGriffithsia sp. (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 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)14,8871
Polymers14,8871
Non-polymers00
Water2,918162
1
A: Griffithsin

A: Griffithsin


Theoretical massNumber of molelcules
Total (without water)29,7742
Polymers29,7742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area4370 Å2
ΔGint-16 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.162, 71.162, 71.488
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Griffithsin / GRFT


Mass: 14887.206 Da / Num. of mol.: 1
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.: 162 / 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: 3.51 Å3/Da / Density % sol: 64.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M bis-tris buffer, pH 6.5 0.1 M magnesium sulfate 3 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: 1.95→30 Å / Num. obs: 15647 / % possible obs: 99.2 % / Redundancy: 10.3 % / Biso Wilson estimate: 16.47 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 49
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 0.101 / Mean I/σ(I) obs: 11.5 / Num. unique obs: 671 / % possible all: 85.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.17.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GUC

2guc


Resolution: 1.95→25.22 Å / SU ML: 0.143 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 16.8842
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1894 1564 10 %
Rwork0.1575 14083 -
obs0.1607 15647 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.81 Å2
Refinement stepCycle: LAST / Resolution: 1.95→25.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms900 0 0 162 1062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192922
X-RAY DIFFRACTIONf_angle_d1.5481246
X-RAY DIFFRACTIONf_chiral_restr0.1223126
X-RAY DIFFRACTIONf_plane_restr0.0095165
X-RAY DIFFRACTIONf_dihedral_angle_d7.5787131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.20891430.14091261X-RAY DIFFRACTION99.79
2.01-2.090.1661370.14651254X-RAY DIFFRACTION100
2.09-2.170.18241400.13641266X-RAY DIFFRACTION100
2.17-2.270.18961380.14021254X-RAY DIFFRACTION100
2.27-2.390.20341410.15541273X-RAY DIFFRACTION100
2.39-2.540.20741450.17221263X-RAY DIFFRACTION100
2.54-2.730.21741360.17581285X-RAY DIFFRACTION100
2.73-3.010.19121450.17041270X-RAY DIFFRACTION100
3.01-3.440.17761430.15971282X-RAY DIFFRACTION100
3.44-4.330.17641450.14431308X-RAY DIFFRACTION100
4.33-25.220.19011510.171367X-RAY DIFFRACTION99.74

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