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- PDB-4j4d: Structure of P51G Cyanovirin-N swapped dimer in the P21212 space group -

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Basic information

Entry
Database: PDB / ID: 4j4d
TitleStructure of P51G Cyanovirin-N swapped dimer in the P21212 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: 2 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 1.4Nov 6, 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
C: Cyanovirin-N
D: Cyanovirin-N
B: Cyanovirin-N


Theoretical massNumber of molelcules
Total (without water)43,9284
Polymers43,9284
Non-polymers00
Water2,828157
1
A: Cyanovirin-N
B: Cyanovirin-N


Theoretical massNumber of molelcules
Total (without water)21,9642
Polymers21,9642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-40 kcal/mol
Surface area10500 Å2
MethodPISA
2
C: Cyanovirin-N
D: Cyanovirin-N


Theoretical massNumber of molelcules
Total (without water)21,9642
Polymers21,9642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-39 kcal/mol
Surface area10480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.313, 62.981, 114.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Cyanovirin-N / CV-N


Mass: 10982.026 Da / Num. of mol.: 4 / 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.: 157 / 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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 40% ethanol, 0.1 M sodium phosphate/citrate, pH 4.2, 5% w/v PEG1000, 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 RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 10, 2011 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→52.31 Å / Num. all: 30944 / Num. obs: 28499 / % possible obs: 92.1 % / Observed criterion σ(F): 3 / Redundancy: 8.75 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.3
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 8.18 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1718 / % possible all: 86.5

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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: 2→52.31 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.716 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.255 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26582 1224 5.1 %RANDOM
Rwork0.21524 ---
obs0.21786 22999 92.34 %-
all-24223 --
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: 53.215 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å2-0 Å2
2--2.35 Å2-0 Å2
3----1.85 Å2
Refinement stepCycle: LAST / Resolution: 2→52.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 0 0 157 3229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213118
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.9364222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1845402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23226.242149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.15415541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4791512
X-RAY DIFFRACTIONr_chiral_restr0.1120.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022344
X-RAY DIFFRACTIONr_mcbond_it0.6991.51991
X-RAY DIFFRACTIONr_mcangle_it1.20323198
X-RAY DIFFRACTIONr_scbond_it1.51631127
X-RAY DIFFRACTIONr_scangle_it2.3154.51023
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 89 -
Rwork0.245 1629 -
obs-1629 91.24 %

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