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- PDB-3a0e: Crystal Structure of Polygonatum cyrtonema lectin (PCL) complexed... -

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Basic information

Entry
Database: PDB / ID: 3a0e
TitleCrystal Structure of Polygonatum cyrtonema lectin (PCL) complexed with dimannoside
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
3alpha-alpha-mannobiose / Mannose/sialic acid-binding lectin
Similarity search - Component
Biological speciesPolygonatum cyrtonema (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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 1.3Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 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)12,7857
Polymers11,9621
Non-polymers8236
Water2,450136
1
A: Mannose/sialic acid-binding lectin
hetero molecules

A: Mannose/sialic acid-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,57014
Polymers23,9252
Non-polymers1,64512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area5320 Å2
ΔGint-134 kcal/mol
Surface area9680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.660, 76.660, 61.401
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: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose / 3alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-3DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 136 / 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: 4.35 Å3/Da / Density % sol: 71.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.0M LiSO4, 2% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Mar 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→45.08 Å / Num. all: 14440 / Num. obs: 14437 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 24.96 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076
Reflection shellResolution: 2→2.11 Å / Redundancy: 14 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 8 / Num. unique all: 2066 / Rsym value: 0.265 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A0D

3a0d


Resolution: 2→45.08 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1468 -RANDOM
Rwork0.19 ---
obs0.19 14437 100 %-
all-14440 --
Displacement parametersBiso max: 69.87 Å2 / Biso mean: 24.4 Å2 / Biso min: 10.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.528 Å20 Å20 Å2
2---1.528 Å20 Å2
3---3.055 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms843 0 48 136 1027
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0055
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_dihedral_angle_d26.66
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.233 140 -
Rwork0.202 --
obs-1422 100 %

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