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- PDB-3a0c: Crystal Structure of an anti-HIV mannose-binding lectin from Poly... -

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Basic information

Entry
Database: PDB / ID: 3a0c
TitleCrystal Structure of an anti-HIV mannose-binding lectin from Polygonatum cyrtonema Hua
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
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 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
B: Mannose/sialic acid-binding lectin
C: Mannose/sialic acid-binding lectin
D: Mannose/sialic acid-binding lectin


Theoretical massNumber of molelcules
Total (without water)47,8494
Polymers47,8494
Non-polymers00
Water1,820101
1
A: Mannose/sialic acid-binding lectin
B: Mannose/sialic acid-binding lectin


Theoretical massNumber of molelcules
Total (without water)23,9252
Polymers23,9252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-20 kcal/mol
Surface area9550 Å2
MethodPISA
2
C: Mannose/sialic acid-binding lectin
D: Mannose/sialic acid-binding lectin


Theoretical massNumber of molelcules
Total (without water)23,9252
Polymers23,9252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-20 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.308, 48.317, 112.221
Angle α, β, γ (deg.)90.00, 90.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Mannose/sialic acid-binding lectin


Mass: 11962.332 Da / Num. of mol.: 4 / Fragment: UNP residues 29-138 / Source method: isolated from a natural source / Source: (natural) Polygonatum cyrtonema (plant) / Strain: Hua / References: UniProt: Q8L568
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 65% MPD, 5mM EDTA, 0.1M HEPES pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 28731 / Num. obs: 28647 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 4.1 / Num. unique all: 4146 / Rsym value: 0.258 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MSA

1msa


Resolution: 2→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: used twin_lsq target, twinning operator= h,-k,-l twinning fraction= 0.398; the twinned data was used for refinement, so no detwinned data is available.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1351 -thin shells, pairs of twin related reflections are in the same set (either working or test)
Rwork0.233 ---
obs0.233 28647 99.7 %-
all-28731 --
Displacement parametersBiso max: 71.92 Å2 / Biso mean: 31.9 Å2 / Biso min: 10.68 Å2
Baniso -1Baniso -2Baniso -3
1--5.308 Å20 Å20.072 Å2
2---4.37 Å20 Å2
3---9.678 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 0 101 3449
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0077
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONo_dihedral_angle_d26.47
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.279 156 -
Rwork0.272 --
obs-2817 97.9 %

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