[English] 日本語
Yorodumi
- PDB-5l6s: Crystal structure of E. coli ADP-glucose pyrophosphorylase (AGPas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l6s
TitleCrystal structure of E. coli ADP-glucose pyrophosphorylase (AGPase) in complex with a positive allosteric regulator beta-fructose-1,6-diphosphate (FBP) - AGPase*FBP
ComponentsGlucose-1-phosphate adenylyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


glucose-1-phosphate adenylyltransferase complex / glucose-1-phosphate adenylyltransferase / glucose-1-phosphate adenylyltransferase activity / glycogen biosynthetic process / AMP binding / protein homotetramerization / magnesium ion binding / ATP binding / identical protein binding
Similarity search - Function
Glucose-1-phosphate adenylyltransferase GlgC, bacterial / ADP-glucose pyrophosphorylase, conserved site / Glucose-1-phosphate adenylyltransferase / ADP-glucose pyrophosphorylase signature 1. / ADP-glucose pyrophosphorylase signature 2. / ADP-glucose pyrophosphorylase signature 3. / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 ...Glucose-1-phosphate adenylyltransferase GlgC, bacterial / ADP-glucose pyrophosphorylase, conserved site / Glucose-1-phosphate adenylyltransferase / ADP-glucose pyrophosphorylase signature 1. / ADP-glucose pyrophosphorylase signature 2. / ADP-glucose pyrophosphorylase signature 3. / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Trimeric LpxA-like superfamily / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1,6-di-O-phosphono-beta-D-fructofuranose / Glucose-1-phosphate adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsCifuente, J.O. / Albesa-Jove, D. / Comino, N. / Madariaga-Marcos, J. / Agirre, J. / Lopez-Fernandez, S. / Garcia-Alija, M. / Guerin, M.E.
CitationJournal: Structure / Year: 2016
Title: Structural Basis of Glycogen Biosynthesis Regulation in Bacteria.
Authors: Cifuente, J.O. / Comino, N. / Madariaga-Marcos, J. / Lopez-Fernandez, S. / Garcia-Alija, M. / Agirre, J. / Albesa-Jove, D. / Guerin, M.E.
History
DepositionMay 31, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 10, 2024Group: 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: Glucose-1-phosphate adenylyltransferase
B: Glucose-1-phosphate adenylyltransferase
C: Glucose-1-phosphate adenylyltransferase
D: Glucose-1-phosphate adenylyltransferase
E: Glucose-1-phosphate adenylyltransferase
F: Glucose-1-phosphate adenylyltransferase
G: Glucose-1-phosphate adenylyltransferase
H: Glucose-1-phosphate adenylyltransferase
I: Glucose-1-phosphate adenylyltransferase
J: Glucose-1-phosphate adenylyltransferase
K: Glucose-1-phosphate adenylyltransferase
L: Glucose-1-phosphate adenylyltransferase
M: Glucose-1-phosphate adenylyltransferase
N: Glucose-1-phosphate adenylyltransferase
O: Glucose-1-phosphate adenylyltransferase
P: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)785,24459
Polymers780,13716
Non-polymers5,10743
Water00
1
A: Glucose-1-phosphate adenylyltransferase
B: Glucose-1-phosphate adenylyltransferase
C: Glucose-1-phosphate adenylyltransferase
D: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,62318
Polymers195,0344
Non-polymers1,58914
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15590 Å2
ΔGint-247 kcal/mol
Surface area60960 Å2
MethodPISA
2
E: Glucose-1-phosphate adenylyltransferase
F: Glucose-1-phosphate adenylyltransferase
G: Glucose-1-phosphate adenylyltransferase
H: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,52717
Polymers195,0344
Non-polymers1,49313
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16060 Å2
ΔGint-229 kcal/mol
Surface area59820 Å2
MethodPISA
3
I: Glucose-1-phosphate adenylyltransferase
J: Glucose-1-phosphate adenylyltransferase
K: Glucose-1-phosphate adenylyltransferase
L: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,86718
Polymers195,0344
Non-polymers1,83314
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16570 Å2
ΔGint-245 kcal/mol
Surface area60820 Å2
MethodPISA
4
M: Glucose-1-phosphate adenylyltransferase
N: Glucose-1-phosphate adenylyltransferase
O: Glucose-1-phosphate adenylyltransferase
P: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,2266
Polymers195,0344
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-68 kcal/mol
Surface area61820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.160, 148.900, 177.490
Angle α, β, γ (deg.)90.00, 113.10, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Glucose-1-phosphate adenylyltransferase / ADP-glucose pyrophosphorylase / ADPGlc PPase / ADP-glucose synthase


Mass: 48758.590 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: glgC, b3430, JW3393 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A6V1, glucose-1-phosphate adenylyltransferase
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: SO4
#3: Sugar
ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 3.60 mM FBP, 2.85mM MgCl2, 20mM HEPES pH=8.0, 100mM NaCl, 22% PEG 4000, 100mM Sodium acetate, 200 mM Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.04→70.29 Å / Num. obs: 146158 / % possible obs: 99 % / Redundancy: 7 % / Biso Wilson estimate: 81.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08382 / Net I/σ(I): 16.75
Reflection shellResolution: 3.04→3.15 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.945 / Mean I/σ(I) obs: 1.93 / % possible all: 98

-
Processing

Software
NameVersionClassification
PHENIX(dev_2219: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YP2

1yp2


Resolution: 3.04→70.745 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 0.11 / Phase error: 29.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2717 14321 4.97 %Random selection
Rwork0.2335 ---
obs0.2354 146136 98.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.04→70.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44781 0 275 0 45056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00245884
X-RAY DIFFRACTIONf_angle_d0.48862598
X-RAY DIFFRACTIONf_dihedral_angle_d11.74127368
X-RAY DIFFRACTIONf_chiral_restr0.0467185
X-RAY DIFFRACTIONf_plane_restr0.0048246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.04-3.07460.4714750.49012X-RAY DIFFRACTION98
3.0746-3.11070.42464820.38659150X-RAY DIFFRACTION98
3.1107-3.14870.40644650.36048969X-RAY DIFFRACTION97
3.1487-3.18850.34354570.33898857X-RAY DIFFRACTION96
3.1885-3.23050.36115060.31298705X-RAY DIFFRACTION93
3.2305-3.27470.37864320.30998811X-RAY DIFFRACTION96
3.2747-3.32150.3465410.30099073X-RAY DIFFRACTION99
3.3215-3.37110.36264830.28359224X-RAY DIFFRACTION100
3.3711-3.42380.3285000.27799240X-RAY DIFFRACTION100
3.4238-3.47990.30874830.26389220X-RAY DIFFRACTION100
3.4799-3.53990.33174190.25899342X-RAY DIFFRACTION100
3.5399-3.60430.30075010.25939168X-RAY DIFFRACTION100
3.6043-3.67360.30244890.2589292X-RAY DIFFRACTION100
3.6736-3.74860.31655310.24759167X-RAY DIFFRACTION100
3.7486-3.83010.2664760.22999188X-RAY DIFFRACTION100
3.8301-3.91920.27244270.22079391X-RAY DIFFRACTION100
3.9192-4.01720.25324910.20979147X-RAY DIFFRACTION100
4.0172-4.12580.25435060.20899298X-RAY DIFFRACTION100
4.1258-4.24720.22774660.20839233X-RAY DIFFRACTION100
4.2472-4.38420.23814390.20119247X-RAY DIFFRACTION100
4.3842-4.54090.21924880.19149192X-RAY DIFFRACTION100
4.5409-4.72270.23465040.19289163X-RAY DIFFRACTION99
4.7227-4.93760.23955180.19969185X-RAY DIFFRACTION99
4.9376-5.19780.26634340.21369199X-RAY DIFFRACTION99
5.1978-5.52340.2714650.23039169X-RAY DIFFRACTION99
5.5234-5.94960.26484350.23258956X-RAY DIFFRACTION97
5.9496-6.5480.26224600.24028510X-RAY DIFFRACTION93
6.548-7.49460.25794200.22689330X-RAY DIFFRACTION100
7.4946-9.43880.225500.20249159X-RAY DIFFRACTION100
9.4388-70.76440.25464780.22729195X-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://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