[English] 日本語
Yorodumi
- PDB-6x84: Sn-glycerol-3-phosphate binding periplasmic protein UgpB from Esc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6x84
TitleSn-glycerol-3-phosphate binding periplasmic protein UgpB from Escherichia coli - W169S, W172S
Componentssn-glycerol-3-phosphate-binding periplasmic protein UgpB
KeywordsCHAPERONE
Function / homology
Function and homology information


glycerophosphodiester transmembrane transport / glycerol-3-phosphate-transporting ATPase complex / glycerol-3-phosphate transmembrane transport / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
Bacterial extracellular solute-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
sn-glycerol-3-phosphate-binding periplasmic protein UgpB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsWu, K. / Zyla, D. / Bardwell, J.C.A.
Funding support United States, Switzerland, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Swiss National Science Foundation310030B_176403/1 Switzerland
Swiss National Science Foundation31003A_156304 Switzerland
CitationJournal: Embo J. / Year: 2020
Title: A metabolite binding protein moonlights as a bile-responsive chaperone.
Authors: Lee, C. / Betschinger, P. / Wu, K. / Zyla, D.S. / Glockshuber, R. / Bardwell, J.C.
History
DepositionJun 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 28, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Oct 18, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: sn-glycerol-3-phosphate-binding periplasmic protein UgpB
B: sn-glycerol-3-phosphate-binding periplasmic protein UgpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2193
Polymers92,1272
Non-polymers921
Water11,818656
1
A: sn-glycerol-3-phosphate-binding periplasmic protein UgpB


Theoretical massNumber of molelcules
Total (without water)46,0641
Polymers46,0641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: sn-glycerol-3-phosphate-binding periplasmic protein UgpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1562
Polymers46,0641
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.936, 46.724, 94.792
Angle α, β, γ (deg.)90.890, 98.530, 105.130
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein sn-glycerol-3-phosphate-binding periplasmic protein UgpB


Mass: 46063.586 Da / Num. of mol.: 2 / Mutation: W169S, W172S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ugpB, b3453, JW3418 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AG80
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 656 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100mM CHES (pH7.5) and 30% PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.000001539413 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000001539413 Å / Relative weight: 1
ReflectionResolution: 1.25→46.8 Å / Num. obs: 370190 / % possible obs: 93 % / Redundancy: 3.598 % / Biso Wilson estimate: 23.085 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.034 / Rrim(I) all: 0.041 / Χ2: 0.909 / Net I/σ(I): 14.04 / Num. measured all: 1332055 / Scaling rejects: 198
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.25-1.283.4331.2120.989013329508262570.5321.44289
1.28-1.323.6861.0091.259597528588260400.6131.18391.1
1.32-1.363.7550.8071.629620827944256230.7340.94391.7
1.36-1.43.720.651.979263827150249000.7960.76191.7
1.4-1.443.6660.5162.448876626278242110.8570.60592.1
1.44-1.493.570.3633.348361525408234200.9180.42892.2
1.49-1.553.3610.2654.37622524406226790.9420.31892.9
1.55-1.613.7080.2055.998200623788221160.9730.2493
1.61-1.693.5560.1567.487485822532210510.9820.18493.4
1.69-1.773.5220.11110.197120721578202180.990.13293.7
1.77-1.863.8040.08214.497375620598193870.9950.09594.1
1.86-1.983.7660.05919.456841819432181660.9970.06993.5
1.98-2.113.6980.04425.36339218282171400.9980.05293.8
2.11-2.283.5740.03630.525746716968160780.9980.04394.8
2.28-2.53.3280.02934.434953515664148860.9990.03595
2.5-2.83.4520.02639.574661614166135030.9990.03195.3
2.8-3.233.4220.02344.484075212468119080.9990.02795.5
3.23-3.953.4720.01950.243558610564102500.9990.02397
3.95-5.593.7050.01754.4229605809679910.9990.0298.7
5.59-46.83.5040.01753.4315297445243660.9990.0298.1

-
Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4aq4

4aq4


Resolution: 1.25→46.8 Å / SU ML: 0.1318 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.304
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1858 9424 5 %
Rwork0.1576 179120 -
obs0.159 188544 94.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.5 Å2
Refinement stepCycle: final / Resolution: 1.25→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6270 0 6 656 6932
Biso mean--33.15 37.72 -
Num. residues----830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01026456
X-RAY DIFFRACTIONf_angle_d1.12158783
X-RAY DIFFRACTIONf_chiral_restr0.0855942
X-RAY DIFFRACTIONf_plane_restr0.00791164
X-RAY DIFFRACTIONf_dihedral_angle_d15.13732303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.260.3162890.30385529X-RAY DIFFRACTION86.67
1.26-1.280.3323020.29725731X-RAY DIFFRACTION91.41
1.28-1.290.33473080.27995857X-RAY DIFFRACTION92.62
1.29-1.310.28493020.25155743X-RAY DIFFRACTION91.91
1.31-1.330.25953080.24215860X-RAY DIFFRACTION92.72
1.33-1.350.28373080.22655837X-RAY DIFFRACTION92.42
1.35-1.370.25013080.22175850X-RAY DIFFRACTION93.08
1.37-1.390.24383090.2135873X-RAY DIFFRACTION93.29
1.39-1.410.24093110.20115894X-RAY DIFFRACTION93.1
1.41-1.430.24713080.19645879X-RAY DIFFRACTION93.81
1.43-1.460.24033130.19035940X-RAY DIFFRACTION93.43
1.46-1.480.23593090.17895860X-RAY DIFFRACTION94
1.48-1.510.21753170.16636016X-RAY DIFFRACTION94.38
1.51-1.540.19083120.15435941X-RAY DIFFRACTION94.24
1.54-1.570.18893130.14675962X-RAY DIFFRACTION94.4
1.57-1.610.20413170.14436003X-RAY DIFFRACTION95.2
1.61-1.650.18563090.14455923X-RAY DIFFRACTION95.22
1.65-1.70.20783200.14466075X-RAY DIFFRACTION95.31
1.7-1.750.1873160.14365981X-RAY DIFFRACTION95.51
1.75-1.80.20013190.14536070X-RAY DIFFRACTION95.9
1.8-1.870.20273190.14636065X-RAY DIFFRACTION96.17
1.87-1.940.17823200.14656072X-RAY DIFFRACTION96.28
1.94-2.030.18293200.1456086X-RAY DIFFRACTION96.58
2.03-2.140.16823200.13936094X-RAY DIFFRACTION96.84
2.14-2.270.18123210.1446098X-RAY DIFFRACTION97.14
2.27-2.450.18923260.14896190X-RAY DIFFRACTION97.4
2.45-2.690.17723230.15416128X-RAY DIFFRACTION97.52
2.69-3.080.17543240.16566162X-RAY DIFFRACTION97.58
3.08-3.880.17613240.15626166X-RAY DIFFRACTION97.76
3.88-46.80.15763290.14646235X-RAY DIFFRACTION98.92

+
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