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- PDB-5gvy: Crystal structure of SALT protein from Oryza sativa -

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Basic information

Entry
Database: PDB / ID: 5gvy
TitleCrystal structure of SALT protein from Oryza sativa
ComponentsSalt stress-induced protein
KeywordsSUGAR BINDING PROTEIN / Salt tolerance / Rice / Mannose binding lectin
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Salt stress-induced protein
Similarity search - Component
Biological speciesOryza sativa subsp. indica (long-grained rice)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.662 Å
AuthorsSharma, P. / Sagar, A. / Kaur, N. / Sharma, I. / Kirat, K. / Ashish, F.N.U. / Pati, P.K.
CitationJournal: Sci Rep / Year: 2020
Title: Structural insights into rice SalTol QTL located SALT protein.
Authors: Kaur, N. / Sagar, A. / Sharma, P. / Pati, P.K.
History
DepositionSep 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Aug 9, 2023Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 8, 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

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Assembly

Deposited unit
A: Salt stress-induced protein
B: Salt stress-induced protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7804
Polymers30,4202
Non-polymers3602
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-7 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.291, 58.811, 51.558
Angle α, β, γ (deg.)90.00, 114.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Salt stress-induced protein / Salt protein / Protein lectin-like / Protein mannose-binding lectin


Mass: 15210.042 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. indica (long-grained rice)
Gene: SALT, ML, OsI_001780 / Variant: Pusa Basmati-1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A2WPN7
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Protein buffer-10mM Sodium phosphate, 1.8mM Potassium phosphate, 137mM NaCl, 2.7mM KCl. Crystallization buffer-200mM NaCl, 100mM Tris pH 8.8, 25% w/v PEG 3350
PH range: 8-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 22, 2016 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. obs: 31076 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 18.35 Å2 / Rmerge(I) obs: 0.033 / Rsym value: 0.033 / Net I/σ(I): 35.8
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 6.071 / % possible all: 76.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1c3m

1c3m


Resolution: 1.662→25.555 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.99
RfactorNum. reflection% reflection
Rfree0.2005 1531 5.04 %
Rwork0.1621 --
obs0.1641 30353 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.662→25.555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 0 24 418 2590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072232
X-RAY DIFFRACTIONf_angle_d0.9123037
X-RAY DIFFRACTIONf_dihedral_angle_d10.7091285
X-RAY DIFFRACTIONf_chiral_restr0.068345
X-RAY DIFFRACTIONf_plane_restr0.006387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6617-1.71530.23421380.18852379X-RAY DIFFRACTION90
1.7153-1.77660.20931320.16812649X-RAY DIFFRACTION99
1.7766-1.84770.23871310.16792636X-RAY DIFFRACTION99
1.8477-1.93180.21241600.16332629X-RAY DIFFRACTION99
1.9318-2.03360.20321200.15342636X-RAY DIFFRACTION99
2.0336-2.16090.18791400.15912673X-RAY DIFFRACTION99
2.1609-2.32770.22881360.16622645X-RAY DIFFRACTION99
2.3277-2.56170.2611230.18182671X-RAY DIFFRACTION99
2.5617-2.93190.20741530.17792630X-RAY DIFFRACTION99
2.9319-3.69220.18971550.1562655X-RAY DIFFRACTION98
3.6922-25.55770.16421430.14692619X-RAY DIFFRACTION96

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