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- PDB-2qsk: Atomic-resolution crystal structure of the Recombinant form of Sc... -

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Basic information

Entry
Database: PDB / ID: 2qsk
TitleAtomic-resolution crystal structure of the Recombinant form of Scytovirin
Componentsscytovirin
KeywordsSUGAR BINDING PROTEIN / lectin
Function / homology: / Scytovirin / regulation of defense response to virus / polysaccharide binding / Scytovirin
Function and homology information
Biological speciesScytonema varium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD/DIRECT REFINEMENT / Resolution: 1 Å
AuthorsMoulaei, T. / Botos, I. / Ziolkowska, N.E. / Dauter, Z. / Wlodawer, A.
CitationJournal: Protein Sci. / Year: 2007
Title: Atomic-resolution crystal structure of the antiviral lectin scytovirin.
Authors: Moulaei, T. / Botos, I. / Ziolkowska, N.E. / Bokesch, H.R. / Krumpe, L.R. / McKee, T.C. / O'Keefe, B.R. / Dauter, Z. / Wlodawer, A.
History
DepositionJul 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE The sequence of this protein was not available at UNP database during the time of ...SEQUENCE The sequence of this protein was not available at UNP database during the time of processing this entry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: scytovirin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9325
Polymers9,7341
Non-polymers1984
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.200, 38.790, 59.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein scytovirin


Mass: 9733.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scytonema varium (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P86041*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1M sodium citrate, 0.1 M imidazole pH 8.0, protein concentration 32 MG/ML 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: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. all: 48601 / Num. obs: 48018 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.057 / Χ2: 0.956 / Net I/σ(I): 19.3
Reflection shellResolution: 1→1.02 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2030 / Χ2: 0.65 / % possible all: 85.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
SHELXSphasing
RefinementMethod to determine structure: SAD/DIRECT REFINEMENT
Starting model: PDB ENTRY 2QT4

2qt4


Resolution: 1→30 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.49 / SU ML: 0.012 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.019 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.147 980 2 %RANDOM
Rwork0.128 ---
obs0.129 47944 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2---0.12 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms674 0 9 129 812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021761
X-RAY DIFFRACTIONr_bond_other_d0.0020.02590
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9441050
X-RAY DIFFRACTIONr_angle_other_deg0.88531433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8545117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82924.68832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.87915113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.269155
X-RAY DIFFRACTIONr_chiral_restr0.0880.299
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02923
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02148
X-RAY DIFFRACTIONr_nbd_refined0.1960.2172
X-RAY DIFFRACTIONr_nbd_other0.2040.2614
X-RAY DIFFRACTIONr_nbtor_refined0.170.2375
X-RAY DIFFRACTIONr_nbtor_other0.0890.2401
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.260.266
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.210
X-RAY DIFFRACTIONr_mcbond_it2.5652659
X-RAY DIFFRACTIONr_mcbond_other1.2032211
X-RAY DIFFRACTIONr_mcangle_it3.1783817
X-RAY DIFFRACTIONr_scbond_it3.5012319
X-RAY DIFFRACTIONr_scangle_it3.6873220
X-RAY DIFFRACTIONr_rigid_bond_restr1.58431698
X-RAY DIFFRACTIONr_sphericity_free12.0363132
X-RAY DIFFRACTIONr_sphericity_bonded4.85831317
LS refinement shellResolution: 1→1.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 69 -
Rwork0.235 2944 -
all-3013 -
obs-2944 85.09 %

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