[English] 日本語
Yorodumi
- PDB-9lfj: Crystal structure of UgpB in complex with G3P -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9lfj
TitleCrystal structure of UgpB in complex with G3P
ComponentsSN-glycerol-3-phophate ABC transporter, periplasmic SN-glycerol-3-phosphate-binding protein
KeywordsTRANSPORT PROTEIN / G1P/G3P transporter substrate-binding protein
Function / homologySN-GLYCEROL-3-PHOSPHATE / :
Function and homology information
Biological speciesPhaeobacter sp. MED193 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsWang, N. / Li, C.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Structural basis and evolutionary pathways of glycerol-1-phosphate transport in marine bacteria.
Authors: Wang, N. / Westermann, L.M. / Li, M. / Li, C. / Murphy, A. / Gu, Z. / Silvano, E. / Blindauer, C.A. / Lidbury, I.D. / Zhang, Y. / Scanlan, D.J. / Chen, Y.
History
DepositionJan 8, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SN-glycerol-3-phophate ABC transporter, periplasmic SN-glycerol-3-phosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5822
Polymers49,4101
Non-polymers1721
Water8,305461
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.450, 115.080, 46.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-957-

HOH

-
Components

#1: Protein SN-glycerol-3-phophate ABC transporter, periplasmic SN-glycerol-3-phosphate-binding protein


Mass: 49409.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence reference for source organism Phaeobacter sp. MED193 is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A3X9J4.
Source: (gene. exp.) Phaeobacter sp. MED193 (bacteria) / Gene: MED193_07903 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3X9J4
#2: Chemical ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.72 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MIB buffer (pH 7.0) and 25% (w/v) PEG 1500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.34→29.01 Å / Num. obs: 83693 / % possible obs: 93 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.4
Reflection shellResolution: 1.34→1.37 Å / Redundancy: 4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3856 / % possible all: 59.2

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→29.01 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1948 4078 4.88 %
Rwork0.1824 --
obs0.183 83629 92.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.34→29.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 0 461 3645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063263
X-RAY DIFFRACTIONf_angle_d0.8664435
X-RAY DIFFRACTIONf_dihedral_angle_d5.019437
X-RAY DIFFRACTIONf_chiral_restr0.074467
X-RAY DIFFRACTIONf_plane_restr0.006584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.360.3029730.30051648X-RAY DIFFRACTION55
1.36-1.370.2981720.29131773X-RAY DIFFRACTION61
1.37-1.390.327890.27271954X-RAY DIFFRACTION67
1.39-1.410.24441030.25722085X-RAY DIFFRACTION71
1.41-1.430.31771210.25972240X-RAY DIFFRACTION78
1.43-1.450.26041470.25862443X-RAY DIFFRACTION83
1.45-1.470.27311340.24682495X-RAY DIFFRACTION87
1.47-1.490.25711280.22752768X-RAY DIFFRACTION92
1.49-1.520.23791380.22252789X-RAY DIFFRACTION96
1.52-1.540.24071390.21792947X-RAY DIFFRACTION99
1.54-1.570.21531390.20782897X-RAY DIFFRACTION100
1.57-1.60.22451520.19892933X-RAY DIFFRACTION100
1.6-1.630.22381810.20682884X-RAY DIFFRACTION100
1.63-1.670.21561490.21192945X-RAY DIFFRACTION100
1.67-1.710.23991320.20462951X-RAY DIFFRACTION100
1.71-1.750.22311670.20432919X-RAY DIFFRACTION100
1.75-1.80.21441620.2032947X-RAY DIFFRACTION100
1.8-1.850.21591450.20552951X-RAY DIFFRACTION100
1.85-1.910.21681530.19442929X-RAY DIFFRACTION100
1.91-1.980.20281310.19212983X-RAY DIFFRACTION100
1.98-2.060.2071610.19132937X-RAY DIFFRACTION100
2.06-2.150.24021430.18022964X-RAY DIFFRACTION100
2.15-2.270.191270.17432989X-RAY DIFFRACTION100
2.27-2.410.18071610.17492974X-RAY DIFFRACTION100
2.41-2.590.18411490.17262995X-RAY DIFFRACTION100
2.59-2.850.17151860.1762958X-RAY DIFFRACTION100
2.85-3.270.17571560.1653023X-RAY DIFFRACTION100
3.27-4.110.18741720.15483041X-RAY DIFFRACTION100
4.11-29.010.14581680.15953189X-RAY DIFFRACTION100

+
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