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- PDB-3a0d: Crystal Structure of Polygonatum cyrtonema lectin (PCL) complexed... -

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Entry
Database: PDB / ID: 3a0d
TitleCrystal Structure of Polygonatum cyrtonema lectin (PCL) complexed with monomannoside
ComponentsMannose/sialic acid-binding lectin
KeywordsSUGAR BINDING PROTEIN / beta-prism II / Lectin
Function / homology
Function and homology information


response to other organism / carbohydrate binding
Similarity search - Function
Agglutinin, subunit A / Bulb-type lectin domain / Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / Orthogonal Prism / Mainly Beta
Similarity search - Domain/homology
methyl alpha-D-mannopyranoside / Mannose/sialic acid-binding lectin
Similarity search - Component
Biological speciesPolygonatum cyrtonema (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDing, J. / Wang, D.C.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Crystal structures of a novel anti-HIV mannose-binding lectin from Polygonatum cyrtonema Hua with unique ligand-binding property and super-structure
Authors: Ding, J. / Bao, J. / Zhu, D. / Zhang, Y. / Wang, D.C.
History
DepositionMar 16, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Jul 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.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mannose/sialic acid-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6377
Polymers11,9621
Non-polymers6746
Water2,036113
1
A: Mannose/sialic acid-binding lectin
hetero molecules

A: Mannose/sialic acid-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,27414
Polymers23,9252
Non-polymers1,34912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area5830 Å2
ΔGint-119 kcal/mol
Surface area9330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.460, 76.460, 61.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Mannose/sialic acid-binding lectin


Mass: 11962.332 Da / Num. of mol.: 1 / Fragment: UNP residues 29-138 / Source method: isolated from a natural source / Source: (natural) Polygonatum cyrtonema (plant) / Strain: HUA / References: UniProt: Q8L568
#2: Sugar ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside / Methylglucoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONFLICT BETWEEN THE SEQUENCE OF THE PROTEIN AND DATABASE (UNP Q8L568; Q8L568_9ASP) MAY BE ...THE CONFLICT BETWEEN THE SEQUENCE OF THE PROTEIN AND DATABASE (UNP Q8L568; Q8L568_9ASP) MAY BE ARISED FROM THE NATURAL MUTATION IN THE PROTEIN OR THE ERRORS IN CDNA SEQEUNCING.

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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: 4.36 Å3/Da / Density % sol: 71.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.0M LiSO4, 2% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→45.17 Å / Num. all: 10912 / Num. obs: 10885 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1566 / Rsym value: 0.349 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A0C

3a0c


Resolution: 2.2→45.16 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1120 -RANDOM
Rwork0.198 ---
obs0.198 10885 99.8 %-
all-10912 --
Displacement parametersBiso max: 68.92 Å2 / Biso mean: 23.2 Å2 / Biso min: 2.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.164 Å20 Å20 Å2
2---1.164 Å20 Å2
3---2.328 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.2→45.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms843 0 38 113 994
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0053
X-RAY DIFFRACTIONc_angle_deg1.43
X-RAY DIFFRACTIONc_dihedral_angle_d26.75
X-RAY DIFFRACTIONc_improper_angle_d0.92
LS refinement shellResolution: 2.2→2.28 Å
RfactorNum. reflection% reflection
Rfree0.309 125 -
Rwork0.246 --
obs-1075 100 %

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