[English] 日本語
Yorodumi
- PDB-4gq7: Crystal structure of Lg-Flo1p -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gq7
TitleCrystal structure of Lg-Flo1p
ComponentsFlocculin
KeywordsSUGAR BINDING PROTEIN / Carbohydrate binding domain / PA14 domain
Function / homology
Function and homology information


flocculation / side of membrane / metal ion binding
Similarity search - Function
Flocculin / Flocculin type 3 repeat / Flocculin repeat / Flocculin type 3 repeat / Jelly Rolls - #1560 / PA14/GLEYA domain / PA14 domain profile. / PA14 domain / PA14 / PA14 domain ...Flocculin / Flocculin type 3 repeat / Flocculin repeat / Flocculin type 3 repeat / Jelly Rolls - #1560 / PA14/GLEYA domain / PA14 domain profile. / PA14 domain / PA14 / PA14 domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsSim, L. / Groes, M. / Olesen, K. / Henriksen, A.
CitationJournal: Febs J. / Year: 2013
Title: Structural and biochemical characterization of the N-terminal domain of flocculin Lg-Flo1p from Saccharomyces pastorianus reveals a unique specificity for phosphorylated mannose.
Authors: Sim, L. / Groes, M. / Olesen, K. / Henriksen, A.
History
DepositionAug 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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
Revision 1.4Sep 13, 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flocculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1534
Polymers24,6701
Non-polymers4823
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.056, 59.947, 82.344
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Flocculin / Lg-Flo1p


Mass: 24670.186 Da / Num. of mol.: 1 / Fragment: UNP residues 26-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces pastorianus (lager yeast)
Strain: CG2164 / Gene: Lg-FLO1 / Plasmid: pPIC-9k / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115 / References: UniProt: B3IUA8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsT173A IS A NATURAL VARIANT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 25% w/v PEG4000, 0.05 M potassium phosphate monobasic, VAPOR DIFFUSION, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.968 Å
DetectorType: BRUKER SMART 1000 / Detector: CCD / Date: Feb 27, 2002
RadiationMonochromator: Triangular single crystal Si(111) with horizontal diffraction plane
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.53→9.99 Å / Num. all: 6260 / Num. obs: 6042 / % possible obs: 97.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 5.9

-
Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XJV

2xjv


Resolution: 2.53→9.99 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.888 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.082 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 282 4.7 %RANDOM
Rwork0.1862 ---
obs0.1888 6041 94.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.67 Å2 / Biso mean: 19.6101 Å2 / Biso min: 5.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.53→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 29 39 1742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021754
X-RAY DIFFRACTIONr_bond_other_d0.0010.021515
X-RAY DIFFRACTIONr_angle_refined_deg1.021.9692405
X-RAY DIFFRACTIONr_angle_other_deg0.7453.0023494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0375219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7632572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68115238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.907152
X-RAY DIFFRACTIONr_chiral_restr0.0620.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212010
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02390
LS refinement shellResolution: 2.53→2.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 18 -
Rwork0.255 386 -
all-404 -
obs--89.58 %

+
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