[English] 日本語
Yorodumi
- PDB-1npl: MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM DAFFODIL (NARCISSUS PSE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1npl
TitleMANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM DAFFODIL (NARCISSUS PSEUDONARCISSUS) BULBS IN COMPLEX WITH MANNOSE-ALPHA1,3-MANNOSE
ComponentsPROTEIN (AGGLUTININ)
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: 2 Å
AuthorsSauerborn, M.K. / Wright, L.M. / Reynolds, C.D. / Grossmann, J.G. / Rizkallah, P.J.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Insights into carbohydrate recognition by Narcissus pseudonarcissus lectin: the crystal structure at 2 A resolution in complex with alpha1-3 mannobiose.
Authors: Sauerborn, M.K. / Wright, L.M. / Reynolds, C.D. / Grossmann, J.G. / Rizkallah, P.J.
History
DepositionDec 17, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 23, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_struct_special_symmetry / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _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 / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (AGGLUTININ)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8648
Polymers12,2101
Non-polymers1,6547
Water1,74797
1
A: PROTEIN (AGGLUTININ)
hetero molecules

A: PROTEIN (AGGLUTININ)
hetero molecules

A: PROTEIN (AGGLUTININ)
hetero molecules

A: PROTEIN (AGGLUTININ)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,45532
Polymers48,8384
Non-polymers6,61628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
MethodPQS
2
A: PROTEIN (AGGLUTININ)
hetero molecules

A: PROTEIN (AGGLUTININ)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,72716
Polymers24,4192
Non-polymers3,30814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area9390 Å2
ΔGint-1 kcal/mol
Surface area10180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.300, 101.200, 37.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-154-

HOH

-
Components

#1: Protein PROTEIN (AGGLUTININ) / DAFFODIL LECTIN


Mass: 12209.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FROM DAFFODIL PLANT FAMILY OF AMARYLLIDACEAE / Source: (natural) Narcissus pseudonarcissus (daffodil) / Organ: BULBS / Strain: DUTCH MASTER / References: GenBank: 289871, 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.: 4
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.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 44 % / Description: ROTATION METHOD
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: VAPOUR DIFFUSION, SITTING DROP, 10 MG/ML IN PBS CONTAINING UP TO 20 MM MANNOBIOSE, EQUILIBRATED AGAINST 40 - 60% AMMONIUM SULPHATE. 17 DEG. C, 4 - 6 DAYS, pH 6.5, vapor diffusion - sitting drop, temperature 290K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 17 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
320 mMalpha-1,3 mannobiose1drop
440-60 %ammonium sulfate1reservoirpH6.5
2phosphate1drop

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 19, 1996 / Details: MIRROR, MONOCHROMATOR
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→60 Å / Num. obs: 9490 / % possible obs: 98.6 % / Redundancy: 2.9 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.07 / Net I/σ(I): 7.26
Reflection shellResolution: 2→2.12 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.276 / % possible all: 98.5
Reflection
*PLUS
Num. measured all: 27588
Reflection shell
*PLUS
% possible obs: 98.6 % / Num. unique obs: 1322 / Num. measured obs: 4005

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→10 Å / SU B: 4.8 / Cross valid method: THROUGHOUT / σ(F): 0
Details: DISORDERED REGION WERE REFINED IN TWO EQUAL CONFORMATIONS (50% OCCUPANCY EACH). NO ATTEMPT WAS MADE AT REFINING THEIR OCCUPANCIES. THE MODEL WAS CHECKED AGAINST ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 457 5 %RANDOM
Rwork0.187 ---
obs-8984 98.6 %-
Displacement parametersBiso mean: 27.6 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms858 0 107 97 1062
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0370.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.042
X-RAY DIFFRACTIONp_mcangle_it2.823
X-RAY DIFFRACTIONp_scbond_it2.082
X-RAY DIFFRACTIONp_scangle_it3.063
X-RAY DIFFRACTIONp_plane_restr0.015
X-RAY DIFFRACTIONp_chiral_restr0.140.15
X-RAY DIFFRACTIONp_singtor_nbd0.1850.3
X-RAY DIFFRACTIONp_multtor_nbd0.2070.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor8.97
X-RAY DIFFRACTIONp_staggered_tor16.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor17.120
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_chiral_restr0.140.15
X-RAY DIFFRACTIONp_mcbond_it2.042
X-RAY DIFFRACTIONp_scbond_it2.082
X-RAY DIFFRACTIONp_mcangle_it2.823
X-RAY DIFFRACTIONp_scangle_it3.063

+
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://pdbjlvh1.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