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- PDB-3ll0: Monomeric Griffithsin with two Gly-Ser Insertions -

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Basic information

Entry
Database: PDB / ID: 3ll0
TitleMonomeric Griffithsin with two Gly-Ser Insertions
ComponentsGriffithsin
KeywordsSUGAR BINDING PROTEIN / lectin / sugar-binding / anti-HIV / high mannose / Man9 / gp120 / gp41 / jacalin-related / Mannose-binding
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-like lectin domain / Jacalin-type lectin domain profile. / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesGriffithsia (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMoulaei, T. / Wlodawer, A.
CitationJournal: Structure / Year: 2010
Title: Monomerization of viral entry inhibitor griffithsin elucidates the relationship between multivalent binding to carbohydrates and anti-HIV activity.
Authors: Moulaei, T. / Shenoy, S.R. / Giomarelli, B. / Thomas, C. / McMahon, J.B. / Dauter, Z. / O'Keefe, B.R. / Wlodawer, A.
History
DepositionJan 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Griffithsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4546
Polymers12,9891
Non-polymers4645
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.1, 55.1, 156.7
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Griffithsin / GRFT


Mass: 12989.062 Da / Num. of mol.: 1 / Mutation: Gly-Ser-Gly-Ser inserted after S16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Griffithsia (eukaryote) / Strain: Q66D336 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P84801
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate, 0.1 M CdCl, 30% w/v PEG 400, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 30, 2009
RadiationMonochromator: VariMax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 16094 / % possible obs: 97.9 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.09 / Χ2: 1.003 / Net I/σ(I): 9.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1478 / Χ2: 0.987 / % possible all: 93.5

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Phasing

Phasing MRRfactor: 40.11 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.75 Å
Translation2.5 Å40.75 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.3phasing
REFMAC5.4.0057refinement
PDB_EXTRACT3.005data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LKY

3lky


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.563 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 936 5.8 %RANDOM
Rwork0.184 ---
obs0.185 15073 97.9 %-
all-16009 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.09 Å2 / Biso mean: 20.174 Å2 / Biso min: 12.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms916 0 29 135 1080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021977
X-RAY DIFFRACTIONr_bond_other_d0.0010.02663
X-RAY DIFFRACTIONr_angle_refined_deg1.8751.9661313
X-RAY DIFFRACTIONr_angle_other_deg0.95431609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4685124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.12423.41541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48115146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.626155
X-RAY DIFFRACTIONr_chiral_restr0.1070.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021100
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02209
X-RAY DIFFRACTIONr_mcbond_it1.0061.5611
X-RAY DIFFRACTIONr_mcbond_other0.3171.5270
X-RAY DIFFRACTIONr_mcangle_it1.7042976
X-RAY DIFFRACTIONr_scbond_it2.8343366
X-RAY DIFFRACTIONr_scangle_it4.3244.5337
LS refinement shellResolution: 1.7→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 71 -
Rwork0.331 1008 -
all-1079 -
obs--92.22 %
Refinement TLS params.Method: refined / Origin x: 16.806 Å / Origin y: 6.271 Å / Origin z: 18.878 Å
111213212223313233
T-0.0222 Å2-0.0005 Å2-0.0025 Å2--0.0302 Å20.0102 Å2---0.0105 Å2
L0.2126 °2-0.1988 °20.3443 °2-1.2672 °2-0.3357 °2--0.8133 °2
S0.0028 Å °-0.0467 Å °0.0058 Å °-0.1318 Å °-0.023 Å °-0.0424 Å °0.0275 Å °-0.0315 Å °0.0203 Å °

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