[English] 日本語
Yorodumi
- PDB-3dzw: Structure of Narcissus pseudonarcissus lectin complex with Mannob... -

+
Open data


ID or keywords:

Loading...

-
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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
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

-
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

-
Phasing

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more