[English] 日本語
Yorodumi
- PDB-5jst: MBP fused MDV1 coiled coil -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jst
TitleMBP fused MDV1 coiled coil
ComponentsMaltose-binding periplasmic protein,Mitochondrial division protein 1
KeywordsPROTEIN BINDING / MBP / Coiled-coil / SER
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / mitochondrial outer membrane / periplasmic space / DNA damage response / membrane
Similarity search - Function
Mitochondrial division protein 1 / Mitochondrial division protein 1 / : / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / G-protein beta WD-40 repeat / WD40 repeat, conserved site ...Mitochondrial division protein 1 / Mitochondrial division protein 1 / : / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
alpha-maltose / ACETATE ION / Mitochondrial division protein 1 / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsKim, B.-W. / Song, H.K.
CitationJournal: Sci Rep / Year: 2017
Title: ACCORD: an assessment tool to determine the orientation of homodimeric coiled-coils.
Authors: Kim, B.W. / Jung, Y.O. / Kim, M.K. / Kwon, D.H. / Park, S.H. / Kim, J.H. / Kuk, Y.B. / Oh, S.J. / Kim, L. / Kim, B.H. / Yang, W.S. / Song, H.K.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / 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_validate_close_contact / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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: Maltose-binding periplasmic protein,Mitochondrial division protein 1
B: Maltose-binding periplasmic protein,Mitochondrial division protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,61010
Polymers97,5382
Non-polymers1,0728
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.515, 102.942, 79.267
Angle α, β, γ (deg.)90.000, 102.510, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A
211chain B

-
Components

#1: Protein Maltose-binding periplasmic protein,Mitochondrial division protein 1 / MBP / MMBP / Maltodextrin-binding protein / Mitochondria fission 2 protein


Mass: 48769.055 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 27-392,UNP RESIDUES 230-300
Source method: isolated from a genetically manipulated source
Details: The fusion protein of MBP and MDV1 (Mitochondrial division protein 1)
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: K12, YJM789 / Gene: malE, b4034, JW3994, MDV1, FIS2, GAG3, NET2, SCY_3176 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: A6ZQL5
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.3~1.7 M Sodium formate, 25% PEG 3350, 0.1 M CaCl2, 0.1 M Sodium acetate/Acetic acid, pH 4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.2553 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2553 Å / Relative weight: 1
ReflectionResolution: 2.199→50 Å / Num. obs: 50774 / % possible obs: 99.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.036 / Rrim(I) all: 0.072 / Χ2: 2.277 / Net I/av σ(I): 35.927 / Net I/σ(I): 15.4 / Num. measured all: 205521
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.244.10.69725360.6960.3930.8011.438100
2.24-2.284.10.61925320.7580.3480.7111.449100
2.28-2.324.10.51725740.830.290.5941.495100
2.32-2.374.10.42925540.8650.2420.4941.517100
2.37-2.424.10.35925700.90.2010.4121.578100
2.42-2.484.10.31725360.920.1780.3641.575100
2.48-2.544.20.26225200.9380.1460.3011.663100
2.54-2.614.10.21725500.9610.1220.251.706100
2.61-2.694.10.17625490.9720.0980.2021.801100
2.69-2.774.10.13825660.9830.0770.1581.835100
2.77-2.874.10.12225390.9850.0690.1411.997100
2.87-2.994.10.125640.9890.0560.1152.235100
2.99-3.124.10.08825540.9920.0490.1012.49100
3.12-3.294.10.07525690.9930.0420.0863.007100
3.29-3.493.90.06825470.9920.0390.0783.382100
3.49-3.763.80.05825700.9950.0340.0683.80199.8
3.76-4.143.80.05425750.9950.0320.0623.97299.7
4.14-4.743.80.04525190.9960.0270.0533.51398.2
4.74-5.9740.0425590.9970.0220.0462.95699.3
5.97-503.80.03622910.9970.0210.0412.74687.1

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DM0, 2XU6

3dm0

2xu6


Resolution: 2.199→36.846 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2736 2011 3.96 %
Rwork0.2249 48755 -
obs0.2268 50766 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.05 Å2 / Biso mean: 60.8294 Å2 / Biso min: 31.49 Å2
Refinement stepCycle: final / Resolution: 2.199→36.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6529 0 86 221 6836
Biso mean--66.67 55.26 -
Num. residues----860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076737
X-RAY DIFFRACTIONf_angle_d0.8799169
X-RAY DIFFRACTIONf_chiral_restr0.0551041
X-RAY DIFFRACTIONf_plane_restr0.0061192
X-RAY DIFFRACTIONf_dihedral_angle_d11.4874011
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3484X-RAY DIFFRACTION7.342TORSIONAL
12B3484X-RAY DIFFRACTION7.342TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1989-2.25390.39611430.333440358399
2.2539-2.31480.33841500.302234943644100
2.3148-2.38290.36341440.291435053649100
2.3829-2.45980.35821370.288134913628100
2.4598-2.54770.34781440.286235183662100
2.5477-2.64970.33161400.282535213661100
2.6497-2.77020.29291390.275834933632100
2.7702-2.91620.31921440.280635053649100
2.9162-3.09880.34671460.284435073653100
3.0988-3.3380.31691540.262135093663100
3.338-3.67360.28631420.230935063648100
3.6736-4.20450.24651460.197235083654100
4.2045-5.29470.22791460.17063480362698
5.2947-36.85070.21171360.18043278341491

+
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