[English] 日本語
Yorodumi
- PDB-3a5p: Crystal structure of hemagglutinin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3a5p
TitleCrystal structure of hemagglutinin
ComponentsHaemagglutinin I
KeywordsSUGAR BINDING PROTEIN / lectin
Function / homologyTumour Suppressor Smad4 - #70 / Hemagglutinin I / Hemagglutinin I / Tumour Suppressor Smad4 / Sandwich / Mainly Beta / Haemagglutinin I
Function and homology information
Biological speciesPhysarum polycephalum (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsWatanabe, N. / Sakai, N. / Nakamura, T. / Nabeshima, Y. / Kouno, T. / Mizuguchi, M. / Kawano, K.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Structure of Physarum polycephalum hemagglutinin I suggests a minimal carbohydrate recognition domain of legume lectin fold
Authors: Kouno, T. / Watanabe, N. / Sakai, N. / Nakamura, T. / Nabeshima, Y. / Morita, M. / Mizuguchi, M. / Aizawa, T. / Demura, M. / Imanaka, T. / Tanaka, I. / Kawano, K.
History
DepositionAug 10, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Haemagglutinin I
B: Haemagglutinin I
C: Haemagglutinin I
D: Haemagglutinin I


Theoretical massNumber of molelcules
Total (without water)43,6004
Polymers43,6004
Non-polymers00
Water15,457858
1
A: Haemagglutinin I
B: Haemagglutinin I


Theoretical massNumber of molelcules
Total (without water)21,8002
Polymers21,8002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-14 kcal/mol
Surface area9010 Å2
MethodPISA
2
C: Haemagglutinin I
D: Haemagglutinin I


Theoretical massNumber of molelcules
Total (without water)21,8002
Polymers21,8002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-12 kcal/mol
Surface area8970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.929, 77.980, 86.109
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Haemagglutinin I


Mass: 10900.101 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physarum polycephalum (eukaryote) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O60949
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 858 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG3350, 150mM NaI, pH 6.5, vapour diffusion, hanging drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.502 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 8, 2006 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.502 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 40006 / % possible obs: 99.8 % / Redundancy: 2.5 % / Biso Wilson estimate: 21.97 Å2 / Rsym value: 0.03 / Net I/σ(I): 49.4
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 11 / Rsym value: 0.161 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: initial model determined by SAD

Resolution: 1.82→30.37 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.423 / SU ML: 0.076 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1999 5 %RANDOM
Rwork0.154 ---
obs0.156 39795 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.48 Å2 / Biso mean: 23.215 Å2 / Biso min: 11.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--1 Å20 Å2
3----1.23 Å2
Refine analyzeLuzzati coordinate error obs: 0.1574 Å / Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.1514 Å
Refinement stepCycle: LAST / Resolution: 1.82→30.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3052 0 0 858 3910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213233
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.9224444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2345438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71424.046131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.93815452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.196159
X-RAY DIFFRACTIONr_chiral_restr0.090.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022517
X-RAY DIFFRACTIONr_nbd_refined0.1840.21489
X-RAY DIFFRACTIONr_nbtor_refined0.30.22190
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2715
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.257
X-RAY DIFFRACTIONr_mcbond_it0.6521.52114
X-RAY DIFFRACTIONr_mcangle_it1.07823333
X-RAY DIFFRACTIONr_scbond_it1.80731298
X-RAY DIFFRACTIONr_scangle_it2.6324.51097
LS refinement shellResolution: 1.819→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 152 -
Rwork0.193 2745 -
all-2897 -
obs--99.76 %

+
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