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- PDB-2gud: Crystal structure of a complex of griffithsin with mannose at 0.9... -

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Basic information

Entry
Database: PDB / ID: 2gud
TitleCrystal structure of a complex of griffithsin with mannose at 0.94 A resolution
Componentsgriffithsin
KeywordsSUGAR BINDING PROTEIN / griffithsin / lectins / domain swapping / mannose binding / HIV / SARS
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 / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
beta-D-mannopyranose / alpha-D-mannopyranose / Griffithsin
Similarity search - Component
Biological speciesGriffithsia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.94 Å
AuthorsZiolkowska, N.E. / Wlodawer, A.
CitationJournal: Structure / Year: 2006
Title: Domain-swapped structure of the potent antiviral protein griffithsin and its mode of carbohydrate binding.
Authors: Ziolkowska, N.E. / O'keefe, B.R. / Mori, T. / Zhu, C. / Giomarelli, B. / Vojdani, F. / Palmer, K.E. / McMahon, J.B. / Wlodawer, A.
History
DepositionApr 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: griffithsin
B: griffithsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,05312
Polymers25,4542
Non-polymers1,59910
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-11 kcal/mol
Surface area9810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.740, 39.440, 57.160
Angle α, β, γ (deg.)90.00, 91.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein griffithsin / GRFT


Mass: 12726.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Griffithsia (eukaryote) / Genus: Griffithsia / Production host: Nicotiana benthamiana (plant) / References: UniProt: P84801

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Sugars , 2 types, 8 molecules

#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: isolated from a genetically manipulated source
Formula: C6H12O6
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: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 444 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8M magnesium sulfate,0.1M MES, 1:10 ratio of griffithsin monomers to mannose, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.7 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 0.94→50 Å / Num. all: 148669 / Num. obs: 148669 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rsym value: 0.064
Reflection shellResolution: 0.94→0.96 Å / % possible all: 75

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
DENZOdata reduction
HKL-2000data scaling
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GTY

2gty


Resolution: 0.94→30 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.543 / SU ML: 0.013 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.018 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15607 1498 1 %RANDOM
Rwork0.1355 ---
all0.1355 148669 --
obs0.1355 148646 95.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.641 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å2-0.35 Å2
2---0.14 Å20 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 0.94→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 105 458 2451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0212031
X-RAY DIFFRACTIONr_bond_other_d0.0020.021722
X-RAY DIFFRACTIONr_angle_refined_deg2.1542.0062738
X-RAY DIFFRACTIONr_angle_other_deg4.86234047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3425242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.723.51691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4815323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2691512
X-RAY DIFFRACTIONr_chiral_restr0.1520.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022191
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02421
X-RAY DIFFRACTIONr_nbd_refined0.2930.2319
X-RAY DIFFRACTIONr_nbd_other0.2310.21811
X-RAY DIFFRACTIONr_nbtor_refined0.1990.21026
X-RAY DIFFRACTIONr_nbtor_other0.1640.21205
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2341
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.268
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9451.51502
X-RAY DIFFRACTIONr_mcbond_other1.131.5523
X-RAY DIFFRACTIONr_mcangle_it2.41821918
X-RAY DIFFRACTIONr_scbond_it3.6453964
X-RAY DIFFRACTIONr_scangle_it4.2734.5819
X-RAY DIFFRACTIONr_rigid_bond_restr1.83834474
X-RAY DIFFRACTIONr_sphericity_free11.3933458
X-RAY DIFFRACTIONr_sphericity_bonded6.48533715
LS refinement shellResolution: 0.938→0.963 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 93 -
Rwork0.257 8303 -
obs--72.5 %

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