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- PDB-4j4g: Structure of P51G Cyanovirin-N swapped tetramer in the C2 space group -

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Basic information

Entry
Database: PDB / ID: 4j4g
TitleStructure of P51G Cyanovirin-N swapped tetramer in the C2 space group
ComponentsCyanovirin-N
KeywordsSUGAR BINDING PROTEIN / CVNH fold / carbohydrate binding protein / antiviral protein
Function / homologyCyanovirin-N / Cyanovirin-N superfamily / CVNH domain / CVNH / regulation of defense response to virus / carbohydrate binding / Cyanovirin-N
Function and homology information
Biological speciesNostoc ellipsosporum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 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

Downloads & links

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Assembly

Deposited unit
A: Cyanovirin-N
C: Cyanovirin-N
B: Cyanovirin-N
D: Cyanovirin-N


Theoretical massNumber of molelcules
Total (without water)43,9284
Polymers43,9284
Non-polymers00
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19030 Å2
ΔGint-110 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.754, 46.232, 117.608
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number5
Space group name H-MC121

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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.: 352 / 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: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.8 M potassium phosphate dibasic, 1.2 M sodium phosphate monobasic, 0.1 M CAPS, pH 10.5, 0.2 M lithium 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 28, 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: 1.92→29.4 Å / Num. all: 40946 / Num. obs: 40086 / % possible obs: 97.9 % / Observed criterion σ(F): 3 / Redundancy: 5.68 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.4
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 3.07 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2643 / % possible all: 89.9

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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: 1.92→29.4 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.203 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.161 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24111 4008 10 %RANDOM
Rwork0.20395 ---
obs0.20763 36065 97.79 %-
all-40073 --
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: 30.363 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å2-0 Å2-0.02 Å2
2--0.14 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.92→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 0 0 352 3424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213150
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9374276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0815414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.31526.267150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86615550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.8191512
X-RAY DIFFRACTIONr_chiral_restr0.1110.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022372
X-RAY DIFFRACTIONr_mcbond_it0.7161.52009
X-RAY DIFFRACTIONr_mcangle_it1.17923237
X-RAY DIFFRACTIONr_scbond_it1.78331141
X-RAY DIFFRACTIONr_scangle_it2.7154.51032
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 273 -
Rwork0.255 2370 -
obs-2370 88.25 %

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