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- PDB-3lly: Crystal Structure Analysis of Maclura pomifera agglutinin -

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Basic information

Entry
Database: PDB / ID: 3lly
TitleCrystal Structure Analysis of Maclura pomifera agglutinin
Components
  • Agglutinin alpha chain
  • Agglutinin beta-2 chain
KeywordsSUGAR BINDING PROTEIN / Maclura pomifera agglutinin / MPA / 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-type lectin domain profile. / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
Agglutinin alpha chain / Agglutinin beta-2 chain
Similarity search - Component
Biological speciesMaclura pomifera (Osage orange)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsHuang, J. / Xu, Z. / Wang, D. / Ogato, C. / Hirama, T. / Palczewski, K. / Hazen, S.L. / Lee, X. / Young, N.M.
CitationJournal: Glycobiology / Year: 2010
Title: Characterization of the secondary binding sites of Maclura pomifera agglutinin by glycan array and crystallographic analyses.
Authors: Huang, J. / Xu, Z. / Wang, D. / Ogata, C.M. / Palczewski, K. / Lee, X. / Young, N.M.
History
DepositionJan 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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: Agglutinin alpha chain
B: Agglutinin beta-2 chain


Theoretical massNumber of molelcules
Total (without water)16,4412
Polymers16,4412
Non-polymers00
Water1,29772
1
A: Agglutinin alpha chain
B: Agglutinin beta-2 chain

A: Agglutinin alpha chain
B: Agglutinin beta-2 chain

A: Agglutinin alpha chain
B: Agglutinin beta-2 chain

A: Agglutinin alpha chain
B: Agglutinin beta-2 chain


Theoretical massNumber of molelcules
Total (without water)65,7668
Polymers65,7668
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area12000 Å2
ΔGint-80 kcal/mol
Surface area24190 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-8 kcal/mol
Surface area8090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.753, 61.753, 149.537
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Agglutinin alpha chain / MPA


Mass: 14768.595 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: from the seeds of the Moraceae plant family / Source: (natural) Maclura pomifera (Osage orange) / References: UniProt: P18674
#2: Protein/peptide Agglutinin beta-2 chain / MPA


Mass: 1672.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: from the seeds of the Moraceae plant family / Source: (natural) Maclura pomifera (Osage orange) / References: UniProt: P18676
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.5M of lithium sulfate, 12% PEG 8000, 1% octyl-beta-D-glucopyranoside, 0.1M Hepes, pH 7.0 in the reservoir solution. The sitting drop is made by protein (28mg/mL) and equal volumn of ...Details: 0.5M of lithium sulfate, 12% PEG 8000, 1% octyl-beta-D-glucopyranoside, 0.1M Hepes, pH 7.0 in the reservoir solution. The sitting drop is made by protein (28mg/mL) and equal volumn of reservoir solution., VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 30, 2000 / Details: mirrors
RadiationMonochromator: KOHZU double crystal monochromator with a sagittally focused second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 8637 / Num. obs: 7981 / % possible obs: 92.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.6 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 35.2
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 14.6 / Num. unique all: 837 / % possible all: 95.1

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.005data extraction
APEXdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JOT

1jot


Resolution: 2.25→20 Å / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 632 6.8 %random
Rwork0.217 ---
all-8608 --
obs-7536 87.5 %-
Solvent computationBsol: 111.6 Å2
Displacement parametersBiso max: 56.86 Å2 / Biso mean: 26.439 Å2 / Biso min: 9.22 Å2
Baniso -1Baniso -2Baniso -3
1--2.684 Å2-14.803 Å20 Å2
2---2.684 Å20 Å2
3---5.367 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1166 0 0 72 1238
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2571.5
X-RAY DIFFRACTIONc_scbond_it1.9682
X-RAY DIFFRACTIONc_mcangle_it1.9782
X-RAY DIFFRACTIONc_scangle_it2.6762.5
LS refinement shellResolution: 2.25→2.33 Å
RfactorNum. reflection% reflection
Rfree0.27 58 -
Rwork0.26 --
obs-654 78.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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