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- PDB-6h2m: Long wavelength Mesh&Collect native SAD phasing on microcrystals -

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Basic information

Entry
Database: PDB / ID: 6h2m
TitleLong wavelength Mesh&Collect native SAD phasing on microcrystals
ComponentsConcanavalin-A,Concanavalin-A
KeywordsSUGAR BINDING PROTEIN / Concanavalin A / Lectin / Long wavelength / Mesh&Collect / Softer X-rays
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 ...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 / SAD / Resolution: 1.929 Å
AuthorsCianci, M. / Nanao, M. / Schneider, T.R.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Long-wavelength Mesh&Collect native SAD phasing from microcrystals.
Authors: Cianci, M. / Nanao, M. / Schneider, T.R.
History
DepositionJul 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,7173
Polymers25,6221
Non-polymers952
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-20 kcal/mol
Surface area10370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.630, 85.670, 88.860
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-419-

HOH

21A-644-

HOH

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Components

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


Mass: 25622.385 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: P02866
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.3 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: drops made from equal amounts of protein solution (1 l, 10 mg/ml in water) and reservoir solution (1l, 34%(v/v) PEG 1500), buffered with 5mM HEPES, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.892 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 13, 2015
RadiationMonochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.892 Å / Relative weight: 1
ReflectionResolution: 1.929→44.43 Å / Num. obs: 34104 / % possible obs: 99.6 % / Redundancy: 18.2 % / CC1/2: 0.999 / Rrim(I) all: 0.148 / Net I/σ(I): 18.89
Reflection shellResolution: 1.929→1.998 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 4.93 / Num. unique obs: 2389 / CC1/2: 0.941 / Rrim(I) all: 0.458 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.929→44.43 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1766 3399 9.97 %
Rwork0.1465 --
obs0.1495 34099 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.929→44.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 0 2 256 2066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031857
X-RAY DIFFRACTIONf_angle_d0.682533
X-RAY DIFFRACTIONf_dihedral_angle_d2.91495
X-RAY DIFFRACTIONf_chiral_restr0.049291
X-RAY DIFFRACTIONf_plane_restr0.003327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.929-1.95660.23231310.18171142X-RAY DIFFRACTION90
1.9566-1.98580.20751280.1551319X-RAY DIFFRACTION100
1.9858-2.01680.2061450.15051277X-RAY DIFFRACTION100
2.0168-2.04990.23311360.14141281X-RAY DIFFRACTION100
2.0499-2.08520.2121510.15431290X-RAY DIFFRACTION100
2.0852-2.12310.18191420.14311261X-RAY DIFFRACTION100
2.1231-2.1640.18581360.14321297X-RAY DIFFRACTION100
2.164-2.20810.21281520.14391287X-RAY DIFFRACTION100
2.2081-2.25610.19611420.14331260X-RAY DIFFRACTION100
2.2561-2.30860.17391310.14221311X-RAY DIFFRACTION100
2.3086-2.36630.20171550.13771278X-RAY DIFFRACTION100
2.3663-2.43030.18451300.14681262X-RAY DIFFRACTION100
2.4303-2.50180.19481460.15431280X-RAY DIFFRACTION100
2.5018-2.58260.21431490.15781309X-RAY DIFFRACTION100
2.5826-2.67490.16811390.15151291X-RAY DIFFRACTION100
2.6749-2.78190.16291370.15611282X-RAY DIFFRACTION100
2.7819-2.90850.20161370.14961283X-RAY DIFFRACTION100
2.9085-3.06180.17051470.14691273X-RAY DIFFRACTION100
3.0618-3.25360.17261570.14251288X-RAY DIFFRACTION100
3.2536-3.50470.15831430.14951276X-RAY DIFFRACTION100
3.5047-3.85730.14591420.13541302X-RAY DIFFRACTION100
3.8573-4.4150.14941410.13331262X-RAY DIFFRACTION100
4.415-5.56070.13291380.12861301X-RAY DIFFRACTION100
5.5607-44.44180.19231440.17291288X-RAY DIFFRACTION100

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