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- PDB-5l6s: Crystal structure of E. coli ADP-glucose pyrophosphorylase (AGPas... -

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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. / : / GlmU-like, C-terminal hexapeptide / Nucleotidyl transferase domain / Nucleotidyl transferase ...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. / : / GlmU-like, C-terminal hexapeptide / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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