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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9lfb
TitleCrystal structure of GpxB in complex with G3P
ComponentsPhosphonate ABC transporter, periplasmic phosphonate-binding protein
KeywordsTRANSPORT PROTEIN / G1P/G3P transporter substrate-binding protein
Function / homologyPhosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein / ABC transporter, phosphonate, periplasmic substrate-binding protein / ATP-binding cassette (ABC) transporter complex / transmembrane transport / SN-GLYCEROL-3-PHOSPHATE / Phosphonate ABC transporter, periplasmic phosphonate-binding protein
Function and homology information
Biological speciesMarinobacter sp. DSM 11874 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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: Phosphonate ABC transporter, periplasmic phosphonate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4472
Polymers35,2751
Non-polymers1721
Water6,449358
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)136.509, 136.509, 136.509
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

-
Components

#1: Protein Phosphonate ABC transporter, periplasmic phosphonate-binding protein


Mass: 35275.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence reference for source organism Marinobacter sp. DSM 11874 is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A1U5Q9.
Source: (gene. exp.) Marinobacter sp. DSM 11874 (bacteria) / Gene: Maqu_3257 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1U5Q9
#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.: 358 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.06 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: calcium acetate, sodium acetate (pH 4.5) and PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→22.75 Å / Num. obs: 28413 / % possible obs: 98.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 16.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.38 / Num. unique obs: 2824 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→22.75 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1937 1438 5.07 %
Rwork0.1751 --
obs0.1761 28349 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→22.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 10 358 2648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072342
X-RAY DIFFRACTIONf_angle_d0.9153179
X-RAY DIFFRACTIONf_dihedral_angle_d6.191315
X-RAY DIFFRACTIONf_chiral_restr0.063342
X-RAY DIFFRACTIONf_plane_restr0.006424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.26431680.20942653X-RAY DIFFRACTION99
2.07-2.150.23221410.19592650X-RAY DIFFRACTION99
2.15-2.250.24581350.1892670X-RAY DIFFRACTION99
2.25-2.370.22591360.19032703X-RAY DIFFRACTION99
2.37-2.520.22261620.18462682X-RAY DIFFRACTION99
2.52-2.710.1991560.20382694X-RAY DIFFRACTION100
2.71-2.980.22021260.1832693X-RAY DIFFRACTION99
2.99-3.410.16651250.17552724X-RAY DIFFRACTION99
3.42-4.30.16911340.1472712X-RAY DIFFRACTION98
4.3-22.140.15721550.16272730X-RAY DIFFRACTION97

+
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