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- PDB-5o6n: High pressure flash cooled concanavalin A -

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Basic information

Entry
Database: PDB / ID: 5o6n
TitleHigh pressure flash cooled concanavalin A
ComponentsConcanavalin-A,Concanavalin-A
KeywordsSUGAR BINDING PROTEIN / high pressure flash cooling / crystal grown without cryoprotectants
Function / homology
Function and homology information


regulation of defense response to virus / D-mannose binding / defense response / metal ion binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsThielmann, Y. / Quirnheim Pais, D.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: A standardized technique for high-pressure cooling of protein crystals.
Authors: Quirnheim Pais, D. / Rathmann, B. / Koepke, J. / Tomova, C. / Wurzinger, P. / Thielmann, Y.
History
DepositionJun 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Concanavalin-A,Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8116
Polymers25,6221
Non-polymers1895
Water7,782432
1
A: Concanavalin-A,Concanavalin-A
hetero molecules

A: Concanavalin-A,Concanavalin-A
hetero molecules

A: Concanavalin-A,Concanavalin-A
hetero molecules

A: Concanavalin-A,Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,24524
Polymers102,4904
Non-polymers75620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area11680 Å2
ΔGint-254 kcal/mol
Surface area32650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.260, 86.230, 89.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

21A-830-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Concanavalin-A,Concanavalin-A / Con A


Mass: 25622.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866

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Non-polymers , 5 types, 437 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10 mg/ml Concanavalin A in 0.025 M HEPES pH 7.0 were mixed in a 1:1 ratio with 6 % (w/v) PEG 8000 and 0.1 M Tris pH 8.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→33.23 Å / Num. obs: 51608 / % possible obs: 98.7 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.04421 / Rrim(I) all: 0.04842 / Net I/σ(I): 21.36
Reflection shellRmerge(I) obs: 0.3805 / Rrim(I) all: 0.4554

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1jbc

1jbc


Resolution: 1.35→33.228 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 16.13
RfactorNum. reflection% reflection
Rfree0.1639 1968 3.87 %
Rwork0.1327 --
obs0.1339 50806 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→33.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 5 432 2246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051998
X-RAY DIFFRACTIONf_angle_d0.8222762
X-RAY DIFFRACTIONf_dihedral_angle_d3.1791465
X-RAY DIFFRACTIONf_chiral_restr0.086324
X-RAY DIFFRACTIONf_plane_restr0.004356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3483-1.3820.24231090.22822751X-RAY DIFFRACTION78
1.382-1.41940.21921280.19723292X-RAY DIFFRACTION93
1.4194-1.46110.20691450.16173448X-RAY DIFFRACTION97
1.4611-1.50830.16921370.13463479X-RAY DIFFRACTION98
1.5083-1.56220.17521410.1263522X-RAY DIFFRACTION99
1.5622-1.62480.18151420.11993488X-RAY DIFFRACTION99
1.6248-1.69870.15991440.12173549X-RAY DIFFRACTION99
1.6987-1.78830.14891400.12623552X-RAY DIFFRACTION100
1.7883-1.90030.16541450.133565X-RAY DIFFRACTION100
1.9003-2.0470.14751430.12043589X-RAY DIFFRACTION100
2.047-2.25290.15921450.12823585X-RAY DIFFRACTION100
2.2529-2.57880.15841480.13653617X-RAY DIFFRACTION100
2.5788-3.24860.17121470.13983631X-RAY DIFFRACTION100
3.2486-33.23810.15031540.12243770X-RAY DIFFRACTION100

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