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- PDB-2qt4: Atomic-resolution crystal structure of the natural form of Scytovirin -

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Basic information

Entry
Database: PDB / ID: 2qt4
TitleAtomic-resolution crystal structure of the natural 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 / Resolution: 1.3 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
DepositionAug 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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


Theoretical massNumber of molelcules
Total (without water)9,7341
Polymers9,7341
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.480, 38.840, 59.720
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 natural source / Source: (natural) Scytonema varium (bacteria) / References: UniProt: P86041*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 30% PEG 8000, 0.2M Li2SO4, 0.1M Na Acetate, pH 4.7, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.3→25 Å / Num. obs: 21876 / % possible obs: 99.2 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.082 / Χ2: 1.598 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
1.3-1.354.520801.72995.8
1.35-1.45.321151.9498.50.666
1.4-1.465.521451.88198.90.48
1.46-1.545.521781.61999.70.34
1.54-1.645.721751.8881000.262
1.64-1.765.821761.5011000.189
1.76-1.94621931.4281000.115
1.94-2.226.122281.3551000.078
2.22-2.86.122311.42799.90.061
2.8-255.723551.38699.10.053

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→19.42 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.576 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.198 939 4.6 %RANDOM
Rwork0.145 ---
obs0.147 20294 92.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.744 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.33 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.3→19.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms699 0 0 115 814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021726
X-RAY DIFFRACTIONr_bond_other_d0.0020.02521
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.94992
X-RAY DIFFRACTIONr_angle_other_deg1.0353.0161253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5125102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36324.51631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3221595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.33155
X-RAY DIFFRACTIONr_chiral_restr0.10.289
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02879
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02140
X-RAY DIFFRACTIONr_nbd_refined0.2060.2161
X-RAY DIFFRACTIONr_nbd_other0.2060.2571
X-RAY DIFFRACTIONr_nbtor_refined0.180.2352
X-RAY DIFFRACTIONr_nbtor_other0.0930.2357
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2710.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.29
X-RAY DIFFRACTIONr_mcbond_it3.5322625
X-RAY DIFFRACTIONr_mcbond_other1.7392205
X-RAY DIFFRACTIONr_mcangle_it4.0163783
X-RAY DIFFRACTIONr_scbond_it4.2422293
X-RAY DIFFRACTIONr_scangle_it4.4263208
X-RAY DIFFRACTIONr_rigid_bond_restr3.1053918
X-RAY DIFFRACTIONr_sphericity_bonded6.33699
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 57 -
Rwork0.286 1087 -
all-1144 -
obs--77.3 %

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