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- PDB-4j4e: Structure of P51G Cyanovirin-N swapped trimer in the P212121 spac... -

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Basic information

Entry
Database: PDB / ID: 4j4e
TitleStructure of P51G Cyanovirin-N swapped trimer in the P212121 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: 2.4 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
B: Cyanovirin-N
E: Cyanovirin-N
C: Cyanovirin-N
D: Cyanovirin-N
F: Cyanovirin-N


Theoretical massNumber of molelcules
Total (without water)65,8926
Polymers65,8926
Non-polymers00
Water23413
1
A: Cyanovirin-N
B: Cyanovirin-N
C: Cyanovirin-N


Theoretical massNumber of molelcules
Total (without water)32,9463
Polymers32,9463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11070 Å2
ΔGint-65 kcal/mol
Surface area15700 Å2
MethodPISA
2
E: Cyanovirin-N
D: Cyanovirin-N
F: Cyanovirin-N


Theoretical massNumber of molelcules
Total (without water)32,9463
Polymers32,9463
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11250 Å2
ΔGint-63 kcal/mol
Surface area15490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.694, 81.006, 137.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Cyanovirin-N / CV-N


Mass: 10982.026 Da / Num. of mol.: 6 / 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.: 13 / 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: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 26% w/v PEG8000, 0.1 M sodium cacodylate, pH 6.5, 0.2 M ammonium sulfate, 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 SATURN 944 / Detector: CCD / Date: Nov 15, 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: 2.4→68.773 Å / Num. all: 27748 / Num. obs: 26277 / % possible obs: 94.7 % / Observed criterion σ(F): 3 / Redundancy: 10.17 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 9.89 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1857 / % possible all: 91.2

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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: 2.4→68.773 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.568 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.5 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28144 1332 5.1 %RANDOM
Rwork0.23672 ---
obs0.23888 24897 94.7 %-
all-26229 --
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: 62.933 Å2
Baniso -1Baniso -2Baniso -3
1--2.32 Å20 Å2-0 Å2
2--2.76 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.4→68.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4608 0 0 13 4621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214668
X-RAY DIFFRACTIONr_angle_refined_deg1.091.9366318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6545600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.32126.216222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.92415810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9171518
X-RAY DIFFRACTIONr_chiral_restr0.0780.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023504
X-RAY DIFFRACTIONr_mcbond_it0.4011.52982
X-RAY DIFFRACTIONr_mcangle_it0.73124788
X-RAY DIFFRACTIONr_scbond_it0.81531686
X-RAY DIFFRACTIONr_scangle_it1.3564.51530
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 110 -
Rwork0.328 1747 -
obs-1747 91.21 %

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