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- PDB-7rib: Griffithsin mutant Y28F/Y68F/Y110F -

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Basic information

Entry
Database: PDB / ID: 7rib
TitleGriffithsin mutant Y28F/Y68F/Y110F
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: 2.1 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

Downloads & links

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Assembly

Deposited unit
A: Griffithsin
B: Griffithsin
C: Griffithsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,67912
Polymers44,3103
Non-polymers1,3699
Water8,377465
1
A: Griffithsin
hetero molecules

A: Griffithsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4538
Polymers29,5402
Non-polymers9136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5860 Å2
ΔGint-38 kcal/mol
Surface area9890 Å2
MethodPISA
2
B: Griffithsin
C: Griffithsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4538
Polymers29,5402
Non-polymers9136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-35 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.201, 47.792, 95.213
Angle α, β, γ (deg.)90.000, 90.561, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

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Components

#1: Protein Griffithsin / GRFT


Mass: 14770.099 Da / Num. of mol.: 3 / Mutation: Y28F, Y68F, Y110F
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.: 6 / 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.01 Å3/Da / Density % sol: 38.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M bis-tris buffer, pH 6.5, 1.0 M ammonium sulfate

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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: May 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 20011 / % possible obs: 96.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 16.41 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 4.8
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.095 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 964 / % possible all: 94.4

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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: 2.1→24.98 Å / SU ML: 0.1907 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.428
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2271 1988 9.94 %
Rwork0.1722 18020 -
obs0.1777 20008 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.73 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 87 465 3225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00182877
X-RAY DIFFRACTIONf_angle_d0.56553882
X-RAY DIFFRACTIONf_chiral_restr0.0421423
X-RAY DIFFRACTIONf_plane_restr0.0032501
X-RAY DIFFRACTIONf_dihedral_angle_d5.8231465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.26211430.19361241X-RAY DIFFRACTION93.39
2.15-2.210.26521250.19041266X-RAY DIFFRACTION94.69
2.21-2.280.25941540.18821243X-RAY DIFFRACTION94.97
2.28-2.350.25461390.18681240X-RAY DIFFRACTION95.04
2.35-2.430.20681330.19141281X-RAY DIFFRACTION95.61
2.43-2.530.24111330.20011292X-RAY DIFFRACTION95.9
2.53-2.650.26771370.18311271X-RAY DIFFRACTION95.85
2.65-2.790.25451440.19611269X-RAY DIFFRACTION96.71
2.79-2.960.24641360.18321291X-RAY DIFFRACTION97.01
2.96-3.190.26041440.17631301X-RAY DIFFRACTION97.18
3.19-3.510.20911500.15181316X-RAY DIFFRACTION97.54
3.51-4.010.17981520.14411297X-RAY DIFFRACTION98.17
4.01-5.050.17721530.13591342X-RAY DIFFRACTION98.48
5.05-24.980.23611450.1871370X-RAY DIFFRACTION98.38

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