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- PDB-3czz: Crystal structure of Cyanovirin-N domain B mutant -

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Basic information

Entry
Database: PDB / ID: 3czz
TitleCrystal structure of Cyanovirin-N domain B mutant
ComponentsCyanovirin-N
KeywordsANTIVIRAL PROTEIN / CYANOVIRIN-N / SUGAR BINDING PROTEIN / HIV-INACTIVATING / GP120 / Protein synthesis inhibitor
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: 1.36 Å
AuthorsMatei, E. / Furey, W. / Gronenborn, A.M.
CitationJournal: Structure / Year: 2008
Title: Solution and crystal structures of a sugar binding site mutant of cyanovirin-N: no evidence of domain swapping.
Authors: Matei, E. / Furey, W. / Gronenborn, A.M.
History
DepositionApr 30, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 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


Theoretical massNumber of molelcules
Total (without water)21,3872
Polymers21,3872
Non-polymers00
Water8,071448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.160, 58.020, 87.790
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: 10693.746 Da / Num. of mol.: 2 / Mutation: E41A, N42A, T57A, R76A, Q78G
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): BL21(DE3) / References: UniProt: P81180
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.04 Å3/Da / Density % sol: 39.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M AMMONIUM ACETATE, 24% POLYETHYLE MONOMETYL ETHER, pH 6.0, 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 / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 14, 2007 / 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: 1.36→29.01 Å / Num. obs: 37884 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.43 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 20.5
Reflection shellResolution: 1.36→1.41 Å / Redundancy: 2.94 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 3.5 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHASER1.3.1phasing
CNS1.1refinement
StructureStudiodata collection
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L5B

1l5b


Resolution: 1.36→29.01 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 995851.91 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.186 3688 9.6 %RANDOM
Rwork0.165 ---
obs0.165 36955 96.4 %-
all-37884 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 250 Å2 / ksol: 0.68 e/Å3
Displacement parametersBiso mean: 11.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.12 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.36→29.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 0 448 1944
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0082
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.52
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.571.5
X-RAY DIFFRACTIONc_mcangle_it0.922
X-RAY DIFFRACTIONc_scbond_it1.53
X-RAY DIFFRACTIONc_scangle_it1.63
LS refinement shellResolution: 1.36→1.45 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.241 564 10.3 %
Rwork0.231 4918 -
obs--87.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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