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- PDB-3dzw: Structure of Narcissus pseudonarcissus lectin complex with Mannob... -

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Basic information

Entry
Database: PDB / ID: 3dzw
TitleStructure of Narcissus pseudonarcissus lectin complex with Mannobiose at 1.7 A resolution, form II
ComponentsAgglutinin
KeywordsSUGAR BINDING PROTEIN / LECTIN / AGGLUTININ / MANNOBIOSE / MANNOSE-ALPHA1 / 3-MANNOSE / DAFFODIL
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 / PHOSPHATE ION / Dimeric mannose specific lectin protein
Similarity search - Component
Biological speciesNarcissus pseudonarcissus (daffodil)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRizkallah, P.J. / Ozbey, S. / Sauerborn, M.K.
CitationJournal: To be Published
Title: Structure of Narcissus pseudonarcissus lectin complex with Mannobiose at 1.7 A resolution, form II
Authors: Rizkallah, P.J. / Ozbey, S. / Sauerborn, M.K.
History
DepositionJul 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / 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 / pdbx_struct_assembly_gen / struct_asym / struct_conn / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Agglutinin
B: Agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,94813
Polymers24,4192
Non-polymers2,52911
Water5,314295
1
A: Agglutinin
hetero molecules

A: Agglutinin
hetero molecules

B: Agglutinin
hetero molecules

B: Agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,89526
Polymers48,8384
Non-polymers5,05722
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
crystal symmetry operation2_664-x+1,-y+1,z-1/21
crystal symmetry operation4_566x,-y+1,-z+11
2
A: Agglutinin
hetero molecules

A: Agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,04314
Polymers24,4192
Non-polymers2,62412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5350 Å2
ΔGint-26 kcal/mol
Surface area10340 Å2
MethodPISA
3
B: Agglutinin
hetero molecules

B: Agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,85312
Polymers24,4192
Non-polymers2,43410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area5590 Å2
ΔGint-20 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.003, 102.011, 74.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 4 / Auth seq-ID: 1 - 109 / Label seq-ID: 1 - 109

Dom-IDAuth asym-IDLabel asym-ID
1BB
2AA

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Components

#1: Protein Agglutinin


Mass: 12209.545 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: bulb / Source: (natural) Narcissus pseudonarcissus (daffodil) / Strain: Dutch Master cultivar / References: UniProt: Q40423*PLUS
#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.: 6
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 293 K / pH: 8
Details: 10 mg/ml in Phosphate buffered saline, containing up to 20mM beta-1,3 mannobiose, pH 8.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.88
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: MIRROR
RadiationMonochromator: SI III SAGITALLY FOCUSED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 1.7→21.031 Å / Num. obs: 30200 / % possible obs: 99.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.382 / % possible all: 99.2

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Phasing

Phasing MRR rigid body: 0.363 / Cor.coef. Fo:Fc: 0.835 / Cor.coef. Io to Ic: 0.684

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
AMoREphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NPL

1npl


Resolution: 1.7→21.031 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.22 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. The Ramachandran plot outliers are a feature of this structure, dictated by the tetrameric oligomerisation, driven by strong ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. The Ramachandran plot outliers are a feature of this structure, dictated by the tetrameric oligomerisation, driven by strong hydrophobicity which causes the deviation.
RfactorNum. reflection% reflectionSelection details
Rfree0.21279 1523 5 %RANDOM
Rwork0.18684 ---
obs0.18823 30180 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2---0.78 Å20 Å2
3---1.48 Å2
Refinement stepCycle: LAST / Resolution: 1.7→21.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 0 163 295 2174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212019
X-RAY DIFFRACTIONr_bond_other_d0.0040.021291
X-RAY DIFFRACTIONr_angle_refined_deg1.5442.0222787
X-RAY DIFFRACTIONr_angle_other_deg2.4613.0013109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.6065238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.4924.10595
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.95315287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.7771515
X-RAY DIFFRACTIONr_chiral_restr0.0950.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022181
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02396
X-RAY DIFFRACTIONr_nbd_refined0.1570.3305
X-RAY DIFFRACTIONr_nbd_other0.1750.31334
X-RAY DIFFRACTIONr_nbtor_refined0.1580.5988
X-RAY DIFFRACTIONr_nbtor_other0.0960.5885
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.5266
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0130.51
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0670.312
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1720.371
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2890.558
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9121488
X-RAY DIFFRACTIONr_mcbond_other0.542470
X-RAY DIFFRACTIONr_mcangle_it2.19931859
X-RAY DIFFRACTIONr_scbond_it3.23841017
X-RAY DIFFRACTIONr_scangle_it4.6496928
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 1399 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.380.5
medium thermal0.492
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 112 -
Rwork0.254 2080 -
obs--99.01 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8710.2635-0.25710.3372-0.09950.23950.0576-0.04150.02530.0472-0.06790.06210.01070.01420.01030.0015-0.0176-0.007-0.0122-0.0074-0.015425.595338.425525.2583
21.07550.0904-0.19070.65240.09240.1410.0817-0.0878-0.10940.0495-0.08670.08470.01380.00780.0050.0062-0.0268-0.0114-0.00240.0112-0.021525.733235.682262.6282
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1091 - 109
2X-RAY DIFFRACTION2BB1 - 1091 - 109

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