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- PDB-3ezm: CYANOVIRIN-N -

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Basic information

Entry
Database: PDB / ID: 3ezm
TitleCYANOVIRIN-N
ComponentsPROTEIN (CYANOVIRIN-N)
KeywordsIMMUNE SYSTEM / CYANOVIRIN-N / HIV-INACTIVATING / DOMAIN-SWAPPING / GP120
Function / homology
Function and homology information


oligosaccharide binding / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsYang, F. / Wlodawer, A.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of cyanovirin-N, a potent HIV-inactivating protein, shows unexpected domain swapping.
Authors: Yang, F. / Bewley, C.A. / Louis, J.M. / Gustafson, K.R. / Boyd, M.R. / Gronenborn, A.M. / Clore, G.M. / Wlodawer, A.
History
DepositionDec 15, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 23, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Sep 6, 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CYANOVIRIN-N)


Theoretical massNumber of molelcules
Total (without water)11,0221
Polymers11,0221
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN (CYANOVIRIN-N)

A: PROTEIN (CYANOVIRIN-N)


Theoretical massNumber of molelcules
Total (without water)22,0442
Polymers22,0442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area6510 Å2
ΔGint-43 kcal/mol
Surface area10850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)48.068, 48.068, 79.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PROTEIN (CYANOVIRIN-N)


Mass: 11022.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc ellipsosporum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P81180
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.39 Å3/Da / Density % sol: 48.2 %
Crystal growpH: 4.4
Details: 26% ISOPROPANOL, 0.1M SODIUM ACETATE, 0.15M CALCIUM CHLORIDE, 5% PEG 400, PH 4.4
Components of the solutions
IDNameCrystal-IDSol-ID
1ISOPROPANOL11
2SODIUM ACETATE11
3PEG 40011
4CACL211
Crystal
*PLUS
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %(v/v)isopropanol1drop
20.1 Msodium acetate1drop
30.2 M1dropCaCl2
426 %(v/v)isopropanol1reservoir
50.1 Msodium acetate1reservoir
60.15 M1reservoirCaCl2
75 %(v/v)PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9795
DetectorType: ADSC / Detector: CCD / Date: Aug 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→10 Å / Num. obs: 17537 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 13.5 Å2 / Rsym value: 0.058 / Net I/σ(I): 9.5
Reflection shellResolution: 1.5→1.54 Å / Rsym value: 0.368 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 107021 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
Rmerge(I) obs: 0.368

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EZM

2ezm


Resolution: 1.5→10 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1608 10.1 %RANDOM
Rwork0.184 ---
obs-15993 91.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.01 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso mean: 17.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20.72 Å20 Å2
2--1.27 Å20 Å2
3----2.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms771 0 0 207 978
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.56
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.161.5
X-RAY DIFFRACTIONx_mcangle_it1.772
X-RAY DIFFRACTIONx_scbond_it2.052
X-RAY DIFFRACTIONx_scangle_it32.5
LS refinement shellResolution: 1.5→1.57 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.209 172 10.1 %
Rwork0.2 1529 -
obs--80.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 10.1 % / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.56
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 1.5 Å / Rfactor Rfree: 0.209 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.2

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