[English] 日本語
Yorodumi
- PDB-5gxt: Crystal structure of PigG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gxt
TitleCrystal structure of PigG
ComponentsMaltose-binding periplasmic protein,PigG
KeywordsPROTEIN TRANSPORT / PigG / Prodigiosin
Function / homology
Function and homology information


detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
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
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Serratia sp. FS14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.245 Å
AuthorsZhang, F. / Ran, T. / Xu, D. / Wang, W.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China31400055 China
National Natural Science Foundation of China31170686 China
National Natural Science Foundation of China31100028 China
the Natural Science Foundation of Jiangsu ProvinceBK20140690 China
CitationJournal: Int. J. Biol. Macromol. / Year: 2017
Title: Crystal structure of MBP-PigG fusion protein and the essential function of PigG in the prodigiosin biosynthetic pathway in Serratia marcescens FS14.
Authors: Zhang, F. / Wei, Q. / Tong, H. / Xu, D. / Wang, W. / Ran, T.
History
DepositionSep 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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,PigG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4152
Polymers51,3911
Non-polymers241
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.700, 60.000, 81.400
Angle α, β, γ (deg.)90.00, 99.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-633-

HOH

-
Components

#1: Protein Maltose-binding periplasmic protein,PigG / MBP / MMBP / Maltodextrin-binding protein


Mass: 51390.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The fusion protein of MBP (RESIDURS 3-368) AND PigG (RESIDUES 369-468)
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Serratia sp. FS14 (bacteria)
Strain: K12 / Gene: malE, b4034, JW3994 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE REFERENCE FOR RESIDUES 369-468 DOES NOT CURRENTLY EXIST IN UNP

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: MgCl2, Tris-HCl, pH 8.5, PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.245→47.221 Å / Num. obs: 21702 / % possible obs: 99.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 4.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.245→47.221 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.296 1076 4.96 %
Rwork0.2298 --
obs0.2332 21702 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.245→47.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3516 0 1 76 3593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143601
X-RAY DIFFRACTIONf_angle_d0.9254884
X-RAY DIFFRACTIONf_dihedral_angle_d15.0232147
X-RAY DIFFRACTIONf_chiral_restr0.053537
X-RAY DIFFRACTIONf_plane_restr0.007637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2448-2.3470.32621320.27662439X-RAY DIFFRACTION95
2.347-2.47070.3611360.27492574X-RAY DIFFRACTION100
2.4707-2.62550.3041140.27262570X-RAY DIFFRACTION99
2.6255-2.82820.37861460.28352612X-RAY DIFFRACTION100
2.8282-3.11270.33591370.26982553X-RAY DIFFRACTION99
3.1127-3.5630.31611390.2412596X-RAY DIFFRACTION100
3.563-4.48850.26481340.19962613X-RAY DIFFRACTION100
4.4885-47.23150.23821380.18252669X-RAY DIFFRACTION99

+
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