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- PDB-6caf: High Resolution Structure of Concanavalin B from Jack Bean (Canav... -

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Basic information

Entry
Database: PDB / ID: 6caf
TitleHigh Resolution Structure of Concanavalin B from Jack Bean (Canavalia ensiformis), A Chitinase-like Protein
ComponentsConcanavalin B
KeywordsPLANT PROTEIN / SEED PROTEIN / chitinase-like protein / MES / Jack Bean
Function / homology
Function and homology information


chitinase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
Chitinase Cts1-like / : / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMcPherson, A.
CitationJournal: To be published
Title: High Resolution Structure of Concanavalin B from Jack Bean (Canavalia ensiformis), a Chitinase-like Protein
Authors: McPherson, A.
History
DepositionJan 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Concanavalin B


Theoretical massNumber of molelcules
Total (without water)36,7631
Polymers36,7631
Non-polymers00
Water6,197344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12340 Å2
Unit cell
Length a, b, c (Å)79.987, 79.987, 101.312
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Concanavalin B / Con B


Mass: 36762.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canavalia ensiformis (jack bean) / Production host: Canavalia ensiformis (jack bean) / References: UniProt: P49347
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.54 Å3/Da / Density % sol: 51.67 % / Description: Extremely elongated hexagonal prisms
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2% saturated ammonium sulfate buffered with Na phosphate at pH 6.5. Room temperature, crystallization in about 1 week. Protein dissolved in 5% NaCl and 0.1 M acetic acid.
PH range: 5.5 7.0

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K-W / Detector: PIXEL / Date: Aug 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.3→101.31 Å / Num. obs: 73116 / % possible obs: 82 % / Redundancy: 51.5 % / CC1/2: 1 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.022 / Rrim(I) all: 0.168 / Rsym value: 0.158 / Net I/av σ(I): 50 / Net I/σ(I): 50.1
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 794 / CC1/2: 0.71 / Rpim(I) all: 0.331 / Rrim(I) all: 0.918 / Rsym value: 0.78 / % possible all: 18.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→69.27 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.836 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12778 3565 4.9 %RANDOM
Rwork0.09574 ---
obs0.09728 69491 81.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å20 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.3→69.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2298 0 0 344 2642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022515
X-RAY DIFFRACTIONr_bond_other_d0.0040.022351
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9613447
X-RAY DIFFRACTIONr_angle_other_deg0.97735445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0395333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08924.219128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08115435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0491518
X-RAY DIFFRACTIONr_chiral_restr0.1110.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212929
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02607
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_it3.1841.7061203
X-RAY DIFFRACTIONr_mcbond_other3.0881.7031202
X-RAY DIFFRACTIONr_mcangle_it3.9732.5741516
X-RAY DIFFRACTIONr_mcangle_other3.9962.5781517
X-RAY DIFFRACTIONr_scbond_it10.7132.31312
X-RAY DIFFRACTIONr_scbond_other10.7152.3041313
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.9513.241911
X-RAY DIFFRACTIONr_long_range_B_refined11.77424.4663079
X-RAY DIFFRACTIONr_long_range_B_other11.03123.3122986
X-RAY DIFFRACTIONr_rigid_bond_restr7.5834866
X-RAY DIFFRACTIONr_sphericity_free51.0385205
X-RAY DIFFRACTIONr_sphericity_bonded24.04554934
LS refinement shellResolution: 1.304→1.338 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 83 -
Rwork0.148 1388 -
obs--22.42 %

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