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- PDB-7v4s: Horcolin complex with methyl-alpha-mannose -

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Basic information

Entry
Database: PDB / ID: 7v4s
TitleHorcolin complex with methyl-alpha-mannose
ComponentsHorcolin
KeywordsSUGAR BINDING PROTEIN / Horcolin / mannose-binding lectin
Function / homology
Function and homology information


apoplast / D-mannose binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily
Similarity search - Domain/homology
methyl alpha-D-mannopyranoside / Horcolin
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsBobbili, K.B. / Sivaji, N. / Jayaprakash, N.G. / Narayanan, V. / Sekhar, A. / Suguna, K. / Surolia, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: Biochemistry / Year: 2022
Title: Structure and Carbohydrate Recognition by the Nonmitogenic Lectin Horcolin.
Authors: Narayanan, V. / Bobbili, K.B. / Sivaji, N. / Jayaprakash, N.G. / Suguna, K. / Surolia, A. / Sekhar, A.
History
DepositionAug 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Horcolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5243
Polymers15,1361
Non-polymers3882
Water3,765209
1
A: Horcolin
hetero molecules

A: Horcolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0496
Polymers30,2722
Non-polymers7774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area1490 Å2
ΔGint-11 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.840, 42.840, 139.201
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1043-

HOH

21A-1083-

HOH

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Components

#1: Protein Horcolin / Agglutinin / Mannose-specific lectin


Mass: 15136.077 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5U9T2
#2: Sugar ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: microbatch
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→46.4 Å / Num. obs: 45978 / % possible obs: 97.3 % / Redundancy: 12 % / Biso Wilson estimate: 11.4 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.038 / Net I/σ(I): 10.5
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 12 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6436 / CC1/2: 0.77 / Rpim(I) all: 0.289 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X1V

1x1v


Resolution: 1.2→37.128 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.049
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2346 2326 5.062 %
Rwork0.2094 43626 -
all0.211 --
obs-45952 96.761 %
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: 13.729 Å2
Baniso -1Baniso -2Baniso -3
1-0.169 Å20.084 Å20 Å2
2--0.169 Å2-0 Å2
3----0.547 Å2
Refinement stepCycle: LAST / Resolution: 1.2→37.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1039 0 26 209 1274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131087
X-RAY DIFFRACTIONr_bond_other_d0.0360.0171014
X-RAY DIFFRACTIONr_angle_refined_deg1.9811.6791476
X-RAY DIFFRACTIONr_angle_other_deg2.4361.6112350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7545142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68421.70741
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67215160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.444155
X-RAY DIFFRACTIONr_chiral_restr0.0920.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021205
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02226
X-RAY DIFFRACTIONr_nbd_refined0.1510.2142
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.2963
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2559
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1110.2513
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2105
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0950.25
X-RAY DIFFRACTIONr_nbd_other0.1760.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.29
X-RAY DIFFRACTIONr_mcbond_it1.3161.162571
X-RAY DIFFRACTIONr_mcbond_other1.3011.16570
X-RAY DIFFRACTIONr_mcangle_it2.0081.746712
X-RAY DIFFRACTIONr_mcangle_other2.0091.748713
X-RAY DIFFRACTIONr_scbond_it2.1531.393516
X-RAY DIFFRACTIONr_scbond_other2.1511.394517
X-RAY DIFFRACTIONr_scangle_it3.2591.999764
X-RAY DIFFRACTIONr_scangle_other3.2572765
X-RAY DIFFRACTIONr_lrange_it5.18824.7954826
X-RAY DIFFRACTIONr_lrange_other4.45523.2564579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.2310.2971860.3043069X-RAY DIFFRACTION94.184
1.231-1.2650.2711420.2763039X-RAY DIFFRACTION94.5039
1.265-1.3020.3211650.292974X-RAY DIFFRACTION95.0636
1.302-1.3420.3131560.2662856X-RAY DIFFRACTION95.3165
1.342-1.3860.2671530.2572810X-RAY DIFFRACTION95.4575
1.386-1.4340.2821380.2552744X-RAY DIFFRACTION96.1628
1.434-1.4880.3111490.2482617X-RAY DIFFRACTION96.2422
1.488-1.5490.2811460.2612538X-RAY DIFFRACTION96.4774
1.549-1.6180.3061160.2432484X-RAY DIFFRACTION96.9787
1.618-1.6970.2691250.2442381X-RAY DIFFRACTION97.2826
1.697-1.7880.269970.232287X-RAY DIFFRACTION97.745
1.788-1.8970.221420.2012120X-RAY DIFFRACTION97.9221
1.897-2.0270.2111380.2132024X-RAY DIFFRACTION98.1389
2.027-2.1890.187960.1991935X-RAY DIFFRACTION98.6401
2.189-2.3980.19900.1671783X-RAY DIFFRACTION98.7348
2.398-2.680.186820.1781638X-RAY DIFFRACTION99.1926
2.68-3.0930.227650.1791473X-RAY DIFFRACTION99.4825
3.093-3.7840.201570.1671242X-RAY DIFFRACTION99.7696
3.784-5.3330.178450.1661016X-RAY DIFFRACTION99.4377
5.333-37.10.284380.238596X-RAY DIFFRACTION100

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