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- PDB-3lky: Monomeric Griffithsin with a Single Gly-Ser Insertion -

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Basic information

Entry
Database: PDB / ID: 3lky
TitleMonomeric Griffithsin with a Single Gly-Ser Insertion
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 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)13,5349
Polymers12,8451
Non-polymers6898
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.6, 48.6, 94.2
Angle α, β, γ (deg.)90, 90, 120
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Griffithsin / GRFT


Mass: 12844.933 Da / Num. of mol.: 1 / Mutation: insertion of Gly-Ser 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M sodium acetate, 0.15 M ammonium sulfate, 25% w/v PEG 3350, pH 4.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 3, 2009
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→30 Å / Num. obs: 48948 / % possible obs: 97.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.063 / Χ2: 1.093 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.1-1.123.50.58324850.78399.7
1.12-1.1440.53124750.83599.3
1.14-1.164.40.50124610.89599.5
1.16-1.184.90.46624800.95499.3
1.18-1.215.30.43124900.98399.1
1.21-1.245.60.41224711.0699.1
1.24-1.275.80.35524691.08599
1.27-1.35.90.324451.00698.7
1.3-1.345.90.2524691.05498.6
1.34-1.3960.19624441.0998.3
1.39-1.4460.15824201.14397.9
1.44-1.496.10.12924611.20497.8
1.49-1.566.10.10924391.32697.4
1.56-1.646.30.09624211.29197
1.64-1.756.50.07824131.27996.6
1.75-1.886.70.06523991.2596.1
1.88-2.076.90.05523841.10395.2
2.07-2.377.20.04923721.11794.5
2.37-2.989.10.06624151.08295.4
2.98-30120.05725351.0199.5

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Phasing

Phasing MRRfactor: 44.68 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å25.17 Å
Translation2.5 Å25.17 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.3phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HYR

2hyr


Resolution: 1.11→25.17 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.982 / WRfactor Rfree: 0.181 / WRfactor Rwork: 0.179 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.901 / SU B: 0.839 / SU ML: 0.02 / SU R Cruickshank DPI: 0.032 / SU Rfree: 0.029 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.03 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.159 1048 2.1 %RANDOM
Rwork0.159 ---
obs0.159 47848 97.9 %-
all-48896 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.46 Å2 / Biso mean: 16.782 Å2 / Biso min: 8.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.05 Å20 Å2
2--0.09 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.11→25.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms906 0 41 117 1064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021994
X-RAY DIFFRACTIONr_bond_other_d0.0020.02677
X-RAY DIFFRACTIONr_angle_refined_deg1.9671.9771337
X-RAY DIFFRACTIONr_angle_other_deg1.01331650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5245122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01523.41541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.51615155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.295155
X-RAY DIFFRACTIONr_chiral_restr0.120.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021086
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02207
X-RAY DIFFRACTIONr_nbd_refined0.1670.2139
X-RAY DIFFRACTIONr_nbd_other0.2040.2671
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2477
X-RAY DIFFRACTIONr_nbtor_other0.0940.2561
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.272
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2950.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.215
X-RAY DIFFRACTIONr_mcbond_it2.4421.5774
X-RAY DIFFRACTIONr_mcbond_other1.8671.5265
X-RAY DIFFRACTIONr_mcangle_it2.9142984
X-RAY DIFFRACTIONr_scbond_it4.2183447
X-RAY DIFFRACTIONr_scangle_it4.9654.5353
X-RAY DIFFRACTIONr_rigid_bond_restr2.39631188
X-RAY DIFFRACTIONr_sphericity_bonded6.1043942
LS refinement shellResolution: 1.11→1.135 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 74 -
Rwork0.298 3406 -
all-3480 -
obs--94.05 %

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