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- PDB-7rkg: Griffithsin mutant Y28W -

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Basic information

Entry
Database: PDB / ID: 7rkg
TitleGriffithsin mutant Y28W
ComponentsGriffithsin
KeywordsSUGAR BINDING PROTEIN / complex / HIV Inhibitor
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: 2.2 Å
AuthorsZhao, G. / Sun, J. / Bewley, C.
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 25, 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

Downloads & links

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Assembly

Deposited unit
A: Griffithsin
B: Griffithsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0434
Polymers29,6822
Non-polymers3602
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-15 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.708, 55.708, 183.035
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Griffithsin / GRFT


Mass: 14841.136 Da / Num. of mol.: 2 / Mutation: Y28W
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.: 2 / 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.: 267 / 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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M citric acid pH 1.5 2.2 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: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 17186 / % possible obs: 97.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 21.21 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.036 / Rrim(I) all: 0.096 / Χ2: 0.342 / Net I/σ(I): 13
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 852 / CC1/2: 0.96 / CC star: 0.99 / Rpim(I) all: 0.105 / Rrim(I) all: 0.239 / Χ2: 0.16 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.17.1-3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2guc

2guc


Resolution: 2.2→29.16 Å / SU ML: 0.1781 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 16.679
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1962 1716 9.99 %
Rwork0.1597 15464 -
obs0.1634 17180 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.19 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 24 267 2083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00671879
X-RAY DIFFRACTIONf_angle_d0.87212541
X-RAY DIFFRACTIONf_chiral_restr0.0566269
X-RAY DIFFRACTIONf_plane_restr0.0043333
X-RAY DIFFRACTIONf_dihedral_angle_d7.1219292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.21321380.16741261X-RAY DIFFRACTION99.93
2.26-2.340.25681500.16981300X-RAY DIFFRACTION100
2.34-2.420.1861450.1731296X-RAY DIFFRACTION99.52
2.42-2.520.22881450.17111253X-RAY DIFFRACTION99.64
2.52-2.630.21851390.17641289X-RAY DIFFRACTION99.37
2.63-2.770.23641390.1731291X-RAY DIFFRACTION98.96
2.77-2.940.22541420.16571284X-RAY DIFFRACTION98.89
2.95-3.170.20791390.16481279X-RAY DIFFRACTION98.47
3.17-3.490.19481500.15681299X-RAY DIFFRACTION97.71
3.49-3.990.15981390.14411292X-RAY DIFFRACTION97.15
4-5.030.15941410.12711294X-RAY DIFFRACTION95.92
5.03-29.160.18351490.18081326X-RAY DIFFRACTION92.3

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