[English] 日本語
Yorodumi
- PDB-3a0c: Crystal Structure of an anti-HIV mannose-binding lectin from Poly... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3a0c
TitleCrystal Structure of an anti-HIV mannose-binding lectin from Polygonatum cyrtonema Hua
ComponentsMannose/sialic acid-binding lectin
KeywordsSUGAR BINDING PROTEIN / beta-prism II / Lectin
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
Mannose/sialic acid-binding lectin
Similarity search - Component
Biological speciesPolygonatum cyrtonema (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDing, J. / Wang, D.C.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Crystal structures of a novel anti-HIV mannose-binding lectin from Polygonatum cyrtonema Hua with unique ligand-binding property and super-structure
Authors: Ding, J. / Bao, J. / Zhu, D. / Zhang, Y. / Wang, D.C.
History
DepositionMar 16, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Nov 1, 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mannose/sialic acid-binding lectin
B: Mannose/sialic acid-binding lectin
C: Mannose/sialic acid-binding lectin
D: Mannose/sialic acid-binding lectin


Theoretical massNumber of molelcules
Total (without water)47,8494
Polymers47,8494
Non-polymers00
Water1,820101
1
A: Mannose/sialic acid-binding lectin
B: Mannose/sialic acid-binding lectin


Theoretical massNumber of molelcules
Total (without water)23,9252
Polymers23,9252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-20 kcal/mol
Surface area9550 Å2
MethodPISA
2
C: Mannose/sialic acid-binding lectin
D: Mannose/sialic acid-binding lectin


Theoretical massNumber of molelcules
Total (without water)23,9252
Polymers23,9252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-20 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.308, 48.317, 112.221
Angle α, β, γ (deg.)90.00, 90.12, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Mannose/sialic acid-binding lectin


Mass: 11962.332 Da / Num. of mol.: 4 / Fragment: UNP residues 29-138 / Source method: isolated from a natural source / Source: (natural) Polygonatum cyrtonema (plant) / Strain: Hua / References: UniProt: Q8L568
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONFLICT BETWEEN THE SEQUENCE OF THE PROTEIN AND DATABASE (UNP Q8L568; Q8L568_9ASP) MAY BE ...THE CONFLICT BETWEEN THE SEQUENCE OF THE PROTEIN AND DATABASE (UNP Q8L568; Q8L568_9ASP) MAY BE ARISED FROM THE NATURAL MUTATION IN THE PROTEIN OR THE ERRORS IN CDNA SEQEUNCING.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 65% MPD, 5mM EDTA, 0.1M HEPES pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 28731 / Num. obs: 28647 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 4.1 / Num. unique all: 4146 / Rsym value: 0.258 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHASERphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MSA

1msa


Resolution: 2→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: used twin_lsq target, twinning operator= h,-k,-l twinning fraction= 0.398; the twinned data was used for refinement, so no detwinned data is available.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1351 -thin shells, pairs of twin related reflections are in the same set (either working or test)
Rwork0.233 ---
obs0.233 28647 99.7 %-
all-28731 --
Displacement parametersBiso max: 71.92 Å2 / Biso mean: 31.9 Å2 / Biso min: 10.68 Å2
Baniso -1Baniso -2Baniso -3
1--5.308 Å20 Å20.072 Å2
2---4.37 Å20 Å2
3---9.678 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 0 101 3449
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0077
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONo_dihedral_angle_d26.47
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.279 156 -
Rwork0.272 --
obs-2817 97.9 %

+
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