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- PDB-2hyr: Crystal structure of a complex of griffithsin with maltose -

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Basic information

Entry
Database: PDB / ID: 2hyr
TitleCrystal structure of a complex of griffithsin with maltose
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-maltose / Griffithsin
Similarity search - Component
Biological speciesGriffithsia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsZiolkowska, N.E. / Wlodawer, A.
CitationJournal: Proteins / Year: 2007
Title: Crystallographic, thermodynamic, and molecular modeling studies of the mode of binding of oligosaccharides to the potent antiviral protein griffithsin.
Authors: Ziolkowska, N.E. / Shenoy, S.R. / O'keefe, B.R. / McMahon, J.B. / Palmer, K.E. / Dwek, R.A. / Wormald, M.R. / Wlodawer, A.
History
DepositionAug 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 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 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details

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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)28,03016
Polymers25,4542
Non-polymers2,57714
Water4,954275
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.820, 53.260, 118.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 8 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
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 283 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 42.99 %
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 maltose, 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: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.51→50 Å / Num. all: 35264 / Num. obs: 35264 / % possible obs: 99.9 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.51→1.56 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345CCDdata collection
HKL-2000data reduction
DENZOdata reduction
HKL-2000data scaling
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GUC

2guc


Resolution: 1.51→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.411 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1854 1764 5 %RANDOM
Rwork0.15229 ---
all0.15395 35264 --
obs0.15395 33427 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.097 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2---0.56 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.51→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 167 275 2240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022071
X-RAY DIFFRACTIONr_bond_other_d0.0010.0191724
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.842800
X-RAY DIFFRACTIONr_angle_other_deg2.8412.8734025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3375242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.62323.44887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52515305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9671511
X-RAY DIFFRACTIONr_chiral_restr0.6440.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022174
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02417
X-RAY DIFFRACTIONr_nbd_refined0.2330.2262
X-RAY DIFFRACTIONr_nbd_other0.1960.21766
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21027
X-RAY DIFFRACTIONr_nbtor_other0.0990.21313
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2176
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0260.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3380.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3090.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2840.248
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6221.51467
X-RAY DIFFRACTIONr_mcbond_other0.4041.5523
X-RAY DIFFRACTIONr_mcangle_it1.99821899
X-RAY DIFFRACTIONr_scbond_it3.35731002
X-RAY DIFFRACTIONr_scangle_it4.3724.5900
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.51→1.551 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 111 -
Rwork0.189 2293 -
obs--95.47 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4051-0.05850.0140.20970.07510.4464-0.0184-0.03360.005-0.01870.0169-0.0117-0.01560.01490.0015-0.02330.00060.0053-0.02220.0044-0.015714.35592.61685.8942
20.5630.1328-0.05620.2640.14740.1341-0.0290.09510.0156-0.0430.03410.03040.0021-0.0283-0.0051-0.0136-0.0029-0.0043-0.02110.0106-0.02097.3459-2.2208-11.9585
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1212 - 122
2X-RAY DIFFRACTION2BB1 - 1212 - 122

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