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- PDB-3hnx: Crystal structure of a designed Cyanovirin-N homolog lectin; LKAM... -

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Basic information

Entry
Database: PDB / ID: 3hnx
TitleCrystal structure of a designed Cyanovirin-N homolog lectin; LKAMG in P212121 space group
ComponentsCyanovirin-N-like protein
KeywordsSUGAR BINDING PROTEIN / Cyanovirin-N / CVNH / lectin
Function / homology
Function and homology information


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
Cyanovirin-N homolog / Cyanovirin-N homolog
Similarity search - Component
Biological speciesTuber borchii (whitish truffle)
Neurospora crassa (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsKoharudin, L.M.I. / Furey, W. / Gronenborn, A.M.
Citation
Journal: Proteins / Year: 2009
Title: A designed chimeric cyanovirin-N homolog lectin: Structure and molecular basis of sucrose binding.
Authors: Koharudin, L.M. / Furey, W. / Gronenborn, A.M.
#1: Journal: Structure / Year: 2008
Title: The Evolutionarily Conserved Family of Cyanovirin-N Homologs: Structures and Carbohydrate Specificity
Authors: Koharudin, L.M.I. / Viscomi, A. / Jee, J. / Ottonello, S. / Gronenborn, A.M.
History
DepositionJun 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyanovirin-N-like protein


Theoretical massNumber of molelcules
Total (without water)12,3861
Polymers12,3861
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.506, 46.204, 50.377
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-like protein


Mass: 12386.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tuber borchii (whitish truffle), (gene. exp.) Neurospora crassa (fungus)
Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5MK11, UniProt: Q7S6U4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 277 K / pH: 8
Details: 50 mg/ml protein concentration in 0.2 M Li2SO4, 0.1 M Tris-HCl (pH 8.5), and 30% PEG 4000 at protein to mother liquor ratio of 8 to 1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 17, 2006 / Details: MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.35→27.26 Å / Num. obs: 23394 / % possible obs: 97.7 % / Observed criterion σ(I): 3 / Redundancy: 13.32 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 40.7
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 2.94 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 2.7 / % possible all: 77.3

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0044refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HNU

3hnu


Resolution: 1.37→27.26 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.643 / SU ML: 0.031 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1168 5.1 %RANDOM
Rwork0.168 ---
obs0.17 21673 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.31 Å2-0 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.37→27.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms932 0 0 151 1083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021955
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.091.9051302
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9845122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.323.60761
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66415154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5891513
X-RAY DIFFRACTIONr_chiral_restr0.0990.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02799
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0971.5578
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.1352933
X-RAY DIFFRACTIONr_scbond_it4.0383377
X-RAY DIFFRACTIONr_scangle_it5.8154.5369
X-RAY DIFFRACTIONr_rigid_bond_restr2.2713955
X-RAY DIFFRACTIONr_sphericity_free9.9443154
X-RAY DIFFRACTIONr_sphericity_bonded6.2113932
LS refinement shellResolution: 1.37→1.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 85 -
Rwork0.396 1504 -
obs--95.32 %

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