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- PDB-2z21: Crystal Structure of a five site mutated Cyanovirin-N -

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Basic information

Entry
Database: PDB / ID: 2z21
TitleCrystal Structure of a five site mutated Cyanovirin-N
ComponentsCyanovirin-N
KeywordsSUGAR BINDING PROTEIN / Cyanovirin-N / Anti-HIV / gp120
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: 1.8 Å
AuthorsFromme, R. / Katilene, Z. / Fromme, P. / Ghirlanda, G.
CitationJournal: Biochemistry / Year: 2007
Title: A Monovalent Mutant of Cyanovirin-N Provides Insight into the Role of Multiple Interactions with gp120 for Antiviral Activity.
Authors: Fromme, R. / Katiliene, Z. / Giomarelli, B. / Bogani, F. / Mahon, J.M. / Mori, T. / Fromme, P. / Ghirlanda, G.
History
DepositionMay 17, 2007Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 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)23,8982
Polymers23,8982
Non-polymers00
Water5,098283
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.457, 38.143, 56.039
Angle α, β, γ (deg.)90.00, 99.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cyanovirin-N / CV-N


Mass: 11949.095 Da / Num. of mol.: 2 / Mutation: K3N, T7A, E23I, P51G, N93A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc ellipsosporum (bacteria) / Gene: Cyanovirin-N / Production host: Escherichia coli (E. coli) / Strain (production host): M51 / References: UniProt: P81180
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 298 K / pH: 6
Details: 30% PEG 8000, 100 MM MGSO4, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 9, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→55.22 Å / Num. obs: 19361 / % possible obs: 87.7 % / Observed criterion σ(I): 4 / Redundancy: 1.9 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.5
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 3.7 / % possible all: 42.3

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Processing

Software
NameVersionClassification
PHASER1.3.1 ARP/WARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LOM

1lom


Resolution: 1.8→31.44 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.498 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R Free: 0.152
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 881 5.2 %RANDOM
Rwork0.164 ---
obs0.167 16077 87.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.35 Å2
2--0.04 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1537 0 0 283 1820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211557
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.231.9322109
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4145202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.59826.16473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83215264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.522156
X-RAY DIFFRACTIONr_chiral_restr0.0860.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021164
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.2686
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21113
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2222
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0871.51036
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49721604
X-RAY DIFFRACTIONr_scbond_it2.1323593
X-RAY DIFFRACTIONr_scangle_it3.2844.5505
X-RAY DIFFRACTIONr_rigid_bond_restr1.54831629
X-RAY DIFFRACTIONr_sphericity_free3.1663283
X-RAY DIFFRACTIONr_sphericity_bonded1.57631537
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 25 -
Rwork0.175 566 -
obs--42.34 %

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