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- PDB-4j4c: Structure of P51G Cyanovirin-N swapped dimer in the P3221 space group -

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Basic information

Entry
Database: PDB / ID: 4j4c
TitleStructure of P51G Cyanovirin-N swapped dimer in the P3221 space group
ComponentsCyanovirin-N
KeywordsSUGAR BINDING PROTEIN / CVNH fold / carbohydrate binding protein / antiviral protein
Function / homology
Function and homology information


regulation of defense response to virus / carbohydrate binding
Similarity search - Function
HIV-inactivating Protein, Cyanovirin-n / Cyanovirin-N / Cyanovirin-N / Cyanovirin-N superfamily / CVNH domain / CVNH / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesNostoc ellipsosporum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKoharudin, L.M.I. / Liu, L. / Gronenborn, A.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Different 3D domain-swapped oligomeric cyanovirin-N structures suggest trapped folding intermediates.
Authors: Koharudin, L.M. / Liu, L. / Gronenborn, A.M.
History
DepositionFeb 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2May 22, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 9, 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: Cyanovirin-N


Theoretical massNumber of molelcules
Total (without water)10,9821
Polymers10,9821
Non-polymers00
Water1,54986
1
A: Cyanovirin-N

A: Cyanovirin-N


Theoretical massNumber of molelcules
Total (without water)21,9642
Polymers21,9642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area6480 Å2
ΔGint-39 kcal/mol
Surface area10800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.928, 47.928, 78.815
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-265-

HOH

21A-286-

HOH

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Components

#1: Protein Cyanovirin-N / CV-N


Mass: 10982.026 Da / Num. of mol.: 1 / Mutation: P51G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc ellipsosporum (bacteria) / Plasmid: pET26B / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P81180
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.38 Å3/Da / Density % sol: 48.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% w/v PEG8000, 0.1 M sodium phosphate/citrate, pH 4.2, 0.2 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 12, 2011 / Details: HF VariMax
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→36.73 Å / Num. all: 8694 / Num. obs: 8659 / % possible obs: 99.6 % / Observed criterion σ(F): 3 / Redundancy: 14.28 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 14.17 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 5 / Num. unique all: 612 / % possible all: 98.1

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0109refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EZM

3ezm


Resolution: 1.9→36.73 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.286 / SU ML: 0.096 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.159 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2273 412 4.8 %RANDOM
Rwork0.19389 ---
obs0.19539 8246 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.744 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20.29 Å2-0 Å2
2--0.58 Å2-0 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms768 0 0 86 854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021791
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.9391074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4725103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.54526.31638
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05515139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.683153
X-RAY DIFFRACTIONr_chiral_restr0.0860.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02596
X-RAY DIFFRACTIONr_mcbond_it0.581.5503
X-RAY DIFFRACTIONr_mcangle_it0.9172811
X-RAY DIFFRACTIONr_scbond_it1.4183288
X-RAY DIFFRACTIONr_scangle_it2.0914.5261
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 24 -
Rwork0.21 588 -
obs-588 98.55 %

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