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- PDB-7exo: Structure of legume lectin domain from Methanocaldococcus jannasc... -

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Basic information

Entry
Database: PDB / ID: 7exo
TitleStructure of legume lectin domain from Methanocaldococcus jannaschii in mannose bound form
ComponentsLegume lectin
KeywordsSUGAR BINDING PROTEIN / legume lectin / lectin / Methanocaldococcus jannaschii
Function / homology
Function and homology information


: / Legume lectin beta-barrel domain / Right handed beta helix domain / Right handed beta helix region / Parallel beta-helix repeat / Parallel beta-helix repeats / : / Pectin lyase fold / Pectin lyase fold/virulence factor / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
ACETATE ION / beta-D-mannopyranose / : / Uncharacterized protein MJ1396
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSuguna, K. / Khan, F.
CitationJournal: Proteins / Year: 2023
Title: Crystal structure of an L-type lectin domain from archaea.
Authors: Khan, F. / Kaza, S.
History
DepositionMay 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 21, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 22, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Legume lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4169
Polymers22,6621
Non-polymers7558
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-11 kcal/mol
Surface area8250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.030, 55.030, 149.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Legume lectin


Mass: 22661.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: DSM 2661 / Gene: MJ1396
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q58791
#3: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 170 molecules

#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.14 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate, pH 4.6 and 2 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→51.624 Å / Num. obs: 24083 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.99 / Net I/σ(I): 9.4
Reflection shellResolution: 1.75→1.78 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1299 / CC1/2: 0.743

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BQP

2bqp


Resolution: 1.75→51.624 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.174 / WRfactor Rwork: 0.153 / SU B: 2.089 / SU ML: 0.065 / Average fsc free: 0.9462 / Average fsc work: 0.9519 / Cross valid method: FREE R-VALUE / ESU R: 0.097 / ESU R Free: 0.092
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1828 1269 5.287 %
Rwork0.1594 22731 -
all0.161 --
obs-24000 99.938 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.486 Å2
Baniso -1Baniso -2Baniso -3
1-0.469 Å2-0 Å2-0 Å2
2--0.469 Å2-0 Å2
3----0.938 Å2
Refinement stepCycle: LAST / Resolution: 1.75→51.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1588 0 46 163 1797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131683
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171460
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.6522305
X-RAY DIFFRACTIONr_angle_other_deg1.5051.5823401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4295210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43725.89778
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38215232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg0.423151
X-RAY DIFFRACTIONr_chiral_restr0.0830.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021902
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02329
X-RAY DIFFRACTIONr_nbd_refined0.2030.2322
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.21428
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2818
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1010.2744
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2141
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.240.211
X-RAY DIFFRACTIONr_nbd_other0.1850.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.29
X-RAY DIFFRACTIONr_mcbond_it1.7041.669838
X-RAY DIFFRACTIONr_mcbond_other1.5021.658835
X-RAY DIFFRACTIONr_mcangle_it2.4282.4881048
X-RAY DIFFRACTIONr_mcangle_other2.2582.4861048
X-RAY DIFFRACTIONr_scbond_it2.9732.085844
X-RAY DIFFRACTIONr_scbond_other2.9712.089845
X-RAY DIFFRACTIONr_scangle_it4.6353.0041257
X-RAY DIFFRACTIONr_scangle_other4.6333.0091258
X-RAY DIFFRACTIONr_lrange_it6.1221.7831900
X-RAY DIFFRACTIONr_lrange_other6.01121.2941865
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.75-1.7950.293970.32316400.32117390.8860.87599.8850.314
1.795-1.8450.288850.24716140.24916990.8710.91000.232
1.845-1.8980.2261000.215490.20216490.9230.9291000.18
1.898-1.9560.22810.17915210.18116020.9410.9411000.16
1.956-2.020.201970.15814270.1615240.9450.9561000.139
2.02-2.0910.171740.14614370.14715110.9590.9671000.13
2.091-2.170.181690.14413890.14614580.9580.9661000.129
2.17-2.2580.174820.14113070.14313890.960.9671000.125
2.258-2.3590.142700.13512970.13513680.9740.97199.92690.119
2.359-2.4740.191640.14212270.14512920.9540.96899.92260.13
2.474-2.6070.178680.15911780.1612460.9580.9621000.145
2.607-2.7650.188560.15911220.1611780.9590.9661000.147
2.765-2.9550.163600.15910360.15910960.9680.9681000.148
2.955-3.1910.188500.1559910.15610410.9650.9711000.15
3.191-3.4940.16620.1339060.1359690.9740.97799.89680.133
3.494-3.9040.174300.1298570.1318880.9670.97899.88740.133
3.904-4.5040.159430.1377400.1387830.9730.9771000.147
4.504-5.5060.155380.1356550.1366930.9790.9831000.148
5.506-7.7420.201260.1945190.1945460.9710.96799.81680.203
7.742-51.6240.171170.2423190.2373440.9830.94197.67440.284

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