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- PDB-3lm1: Crystal Structure Analysis of Maclura pomifera agglutinin complex... -

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Basic information

Entry
Database: PDB / ID: 3lm1
TitleCrystal Structure Analysis of Maclura pomifera agglutinin complex with p-nitrophenyl-GalNAc
Components
  • Agglutinin alpha chain
  • Agglutinin beta-2 chain
KeywordsSUGAR BINDING PROTEIN / Maclura pomifera agglutinin / MPA / MPA complex / (p)-nitrophenyl-GalNAc / 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
Chem-LEC / Agglutinin alpha chain / Agglutinin beta-2 chain
Similarity search - Component
Biological speciesMaclura pomifera (Osage orange)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.2Jul 29, 2020Group: Advisory / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / 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 1.3Sep 6, 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: Agglutinin alpha chain
B: Agglutinin beta-2 chain
C: Agglutinin alpha chain
D: Agglutinin beta-2 chain
E: Agglutinin alpha chain
F: Agglutinin beta-2 chain
G: Agglutinin alpha chain
H: Agglutinin beta-2 chain
I: Agglutinin alpha chain
J: Agglutinin beta-2 chain
K: Agglutinin alpha chain
L: Agglutinin beta-2 chain
M: Agglutinin alpha chain
N: Agglutinin beta-2 chain
O: Agglutinin alpha chain
P: Agglutinin beta-2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,47123
Polymers131,07516
Non-polymers2,3967
Water15,835879
1
A: Agglutinin alpha chain
B: Agglutinin beta-2 chain
E: Agglutinin alpha chain
F: Agglutinin beta-2 chain
I: Agglutinin alpha chain
J: Agglutinin beta-2 chain
M: Agglutinin alpha chain
N: Agglutinin beta-2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,90712
Polymers65,5388
Non-polymers1,3694
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11600 Å2
ΔGint-80 kcal/mol
Surface area23680 Å2
MethodPISA
2
C: Agglutinin alpha chain
D: Agglutinin beta-2 chain
G: Agglutinin alpha chain
H: Agglutinin beta-2 chain
K: Agglutinin alpha chain
L: Agglutinin beta-2 chain
O: Agglutinin alpha chain
P: Agglutinin beta-2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,56411
Polymers65,5388
Non-polymers1,0273
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11630 Å2
ΔGint-81 kcal/mol
Surface area23520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.090, 133.290, 200.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsIn one asymmetric unit, there are two agglutinin tetramers

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Components

#1: Protein
Agglutinin alpha chain / MPA


Mass: 14768.595 Da / Num. of mol.: 8 / 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: 1615.790 Da / Num. of mol.: 8 / 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: Sugar
ChemComp-LEC / 4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside / N-[(2S,3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-(4-nitrophenoxy)oxan-3-yl]ethanamide / 4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucoside / 4-nitrophenyl 2-acetamido-2-deoxy-D-glucoside / 4-nitrophenyl 2-acetamido-2-deoxy-glucoside


Type: D-saccharide / Mass: 342.301 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H18N2O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 879 / 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: 3.53 Å3/Da / Density % sol: 65.18 %
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 in the presence of p-nitrophenyl-alpha-GalNAc., 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: 1.9→29.8 Å / Num. all: 145978 / Num. obs: 122330 / % possible obs: 83.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 24.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.5 / Num. unique all: 6716 / % possible all: 46.6

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
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: 2.1→20 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 9650 8.9 %random
Rwork0.223 ---
all0.244 108366 --
obs0.223 99067 91.4 %-
Solvent computationBsol: 46.941 Å2
Displacement parametersBiso max: 58.73 Å2 / Biso mean: 26.595 Å2 / Biso min: 9.11 Å2
Baniso -1Baniso -2Baniso -3
1-2.508 Å20 Å20 Å2
2---0.445 Å20 Å2
3----2.064 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9263 0 168 879 10310
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1431.5
X-RAY DIFFRACTIONc_scbond_it1.8042
X-RAY DIFFRACTIONc_mcangle_it1.762
X-RAY DIFFRACTIONc_scangle_it2.6222.5
LS refinement shellResolution: 2.1→2.11 Å
RfactorNum. reflection% reflection
Rfree0.2681 136 -
Rwork0.2404 --
obs-1254 88.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2test\npg.par
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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