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- PDB-6x7h: Cyanovirin-N Mutation I34Y with Dimannose bound -

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Basic information

Entry
Database: PDB / ID: 6x7h
TitleCyanovirin-N Mutation I34Y with Dimannose bound
ComponentsCyanovirin-N
KeywordsANTIVIRAL PROTEIN / Mannose binding protein Antiviral protein
Function / homologyCyanovirin-N / Cyanovirin-N superfamily / CVNH domain / CVNH / regulation of defense response to virus / carbohydrate binding / 2alpha-alpha-mannobiose / Cyanovirin-N
Function and homology information
Biological speciesNostoc ellipsosporum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsFromme, R. / Sharma, P. / Ghirlanda, G.
Citation
Journal: Elife / Year: 2022
Title: Design of novel cyanovirin-N variants by modulation of binding dynamics through distal mutations.
Authors: Kazan, I.C. / Sharma, P. / Rahman, M.I. / Bobkov, A. / Fromme, R. / Ghirlanda, G. / Ozkan, S.B.
#1: Journal: Protein Sci. / Year: 2008
Title: Conformational gating of dimannose binding to the antiviral protein cyanovirin revealed from the crystal structure at 1.35 A resolution.
Authors: Fromme, R. / Katiliene, Z. / Fromme, P. / Ghirlanda, G.
#2: Journal: Biochemistry / Year: 2007
Title: A monovalent mutant of cyanovirin-N provides insight into the role of multiple interactions with gp120 for antiviral activity.
Authors: Fromme, R. / Katiliene, Z. / Giomarelli, B. / Bogani, F. / Mc Mahon, J. / Mori, T. / Fromme, P. / Ghirlanda, G.
History
DepositionMay 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyanovirin-N
B: Cyanovirin-N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6834
Polymers23,9982
Non-polymers6852
Water5,332296
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint13 kcal/mol
Surface area9730 Å2
Unit cell
Length a, b, c (Å)49.724, 38.011, 55.867
Angle α, β, γ (deg.)90.000, 100.000, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Cyanovirin-N / CV-N


Mass: 11999.111 Da / Num. of mol.: 2 / Mutation: I34Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc ellipsosporum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P81180
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.17 Å3/Da / Density % sol: 43.23 % / Description: Needle, 200 by 50 um
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 2 M ammonium sulfate, 5% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2018
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.25→15.43 Å / Num. obs: 52827 / % possible obs: 92.7 % / Redundancy: 3.5 % / CC1/2: 0.991 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.053 / Rrim(I) all: 0.098 / Net I/σ(I): 9.6 / Num. measured all: 185048 / Scaling rejects: 87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.25-1.273.10.738835426850.5940.4820.8851.695
6.85-15.431.20.13798850.9680.1330.19116.823

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSVERSION Jan 26, 2018data reduction
Aimless7.0.62data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2RDK

2rdk


Resolution: 1.25→15.43 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1734 1564 2.96 %
Rwork0.1403 51237 -
obs0.1413 52801 92.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.07 Å2 / Biso mean: 17.9278 Å2 / Biso min: 8.2 Å2
Refinement stepCycle: final / Resolution: 1.25→15.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1508 0 88 296 1892
Biso mean--17.15 35.27 -
Num. residues----200
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.25-1.290.24721470.24444815496297
1.29-1.340.20691500.203450325182100
1.34-1.390.2151480.179150095157100
1.39-1.450.19361480.151350165164100
1.45-1.530.17281440.130150255169100
1.53-1.630.15791700.12249865156100
1.63-1.750.15881510.120950285179100
1.75-1.930.14271560.113250365192100
1.93-2.20.13681580.11150215179100
2.2-2.770.18611390.14134820495994
2.78-15.430.2096530.17751449150228

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