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- PDB-5mni: Escherichia coli AGPase mutant R130A apo form -

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Basic information

Entry
Database: PDB / ID: 5mni
TitleEscherichia coli AGPase mutant R130A apo form
ComponentsGlucose-1-phosphate adenylyltransferase
KeywordsTRANSFERASE / EC. 2.7.7.27 Glycogen biosynthesis ADP-glucose pyrophosphorilase Nucleotidyltransferase
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
Glucose-1-phosphate adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsCifuente, J.O. / Comino, N. / Marina, A. / Orrantia, A. / Eguskiza, A. / Guerin, M.E.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Mechanistic insights into the allosteric regulation of bacterial ADP-glucose pyrophosphorylases.
Authors: Comino, N. / Cifuente, J.O. / Marina, A. / Orrantia, A. / Eguskiza, A. / Guerin, M.E.
History
DepositionDec 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
E: Glucose-1-phosphate adenylyltransferase
G: Glucose-1-phosphate adenylyltransferase
H: Glucose-1-phosphate adenylyltransferase
F: Glucose-1-phosphate adenylyltransferase
A: Glucose-1-phosphate adenylyltransferase
B: Glucose-1-phosphate adenylyltransferase
D: Glucose-1-phosphate adenylyltransferase
C: Glucose-1-phosphate adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)389,3808
Polymers389,3808
Non-polymers00
Water00
1
A: Glucose-1-phosphate adenylyltransferase
B: Glucose-1-phosphate adenylyltransferase
D: Glucose-1-phosphate adenylyltransferase
C: Glucose-1-phosphate adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)194,6904
Polymers194,6904
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12380 Å2
ΔGint-52 kcal/mol
Surface area58970 Å2
MethodPISA
2
E: Glucose-1-phosphate adenylyltransferase
G: Glucose-1-phosphate adenylyltransferase
H: Glucose-1-phosphate adenylyltransferase
F: Glucose-1-phosphate adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)194,6904
Polymers194,6904
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12290 Å2
ΔGint-47 kcal/mol
Surface area60190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.224, 147.603, 125.572
Angle α, β, γ (deg.)90.00, 91.52, 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: 48672.473 Da / Num. of mol.: 8 / Mutation: R130A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: glgC, b3430, JW3393 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A6V1, glucose-1-phosphate adenylyltransferase

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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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Sitting drop 96 MRC2 well plates using a mosquito crystal robot (TTP Labtech). Crystals were obtained by mixing 0.25 ul of E coli AGPase_R130A at 6.3 mg/ml in 50 mM Tris-HCl pH 7.5, 100 mM ...Details: Sitting drop 96 MRC2 well plates using a mosquito crystal robot (TTP Labtech). Crystals were obtained by mixing 0.25 ul of E coli AGPase_R130A at 6.3 mg/ml in 50 mM Tris-HCl pH 7.5, 100 mM NaCl with 0.25 ul of mother liquor containing 14% polyethylene glycol 3.350, 140 mM magnesium formate, 30% ethylene glycol. Crystals grew in 13 days and were frozen under liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.09→73.8 Å / Num. obs: 62893 / % possible obs: 99 % / Redundancy: 3.3 % / Biso Wilson estimate: 84.78 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08515 / Net I/σ(I): 8.86
Reflection shellResolution: 3.09→3.201 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.9436 / Mean I/σ(I) obs: 1.23 / CC1/2: 0.524 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: E coli AGPase tetramer

Resolution: 3.09→73.8 Å / SU ML: 0.51 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 31.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2727 3163 5.05 %
Rwork0.2354 --
obs0.2373 62619 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.09→73.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23701 0 0 0 23701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00524215
X-RAY DIFFRACTIONf_angle_d0.68233028
X-RAY DIFFRACTIONf_dihedral_angle_d15.5938445
X-RAY DIFFRACTIONf_chiral_restr0.0513790
X-RAY DIFFRACTIONf_plane_restr0.0064321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0903-3.13640.40761400.3892563X-RAY DIFFRACTION98
3.1364-3.18550.41671340.38032535X-RAY DIFFRACTION99
3.1855-3.23770.40851470.36832584X-RAY DIFFRACTION99
3.2377-3.29350.41481330.35952506X-RAY DIFFRACTION99
3.2935-3.35340.35491420.33842570X-RAY DIFFRACTION99
3.3534-3.41790.34821620.32162536X-RAY DIFFRACTION100
3.4179-3.48770.31571370.30292614X-RAY DIFFRACTION100
3.4877-3.56350.35031130.29242575X-RAY DIFFRACTION100
3.5635-3.64640.33711320.29572608X-RAY DIFFRACTION100
3.6464-3.73760.27551310.2772577X-RAY DIFFRACTION100
3.7376-3.83860.28831370.2542574X-RAY DIFFRACTION100
3.8386-3.95160.2821300.23822614X-RAY DIFFRACTION100
3.9516-4.07910.28781130.23442617X-RAY DIFFRACTION100
4.0791-4.22490.24571320.22572575X-RAY DIFFRACTION100
4.2249-4.3940.26111470.20722593X-RAY DIFFRACTION100
4.394-4.5940.21561270.19152596X-RAY DIFFRACTION100
4.594-4.83610.23841320.1882604X-RAY DIFFRACTION100
4.8361-5.13910.25211460.19672596X-RAY DIFFRACTION100
5.1391-5.53570.26511520.20572590X-RAY DIFFRACTION100
5.5357-6.09260.26181400.22122585X-RAY DIFFRACTION100
6.0926-6.97360.27321540.22582613X-RAY DIFFRACTION100
6.9736-8.78370.21941370.19812610X-RAY DIFFRACTION100
8.7837-73.80.22281450.1962621X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 67.7114 Å / Origin y: 72.2377 Å / Origin z: 94.4025 Å
111213212223313233
T0.4213 Å20.0214 Å2-0.0084 Å2-0.5138 Å20.0067 Å2--0.4335 Å2
L0.1446 °20.154 °2-0.0333 °2-0.8188 °2-0.3632 °2--0.2057 °2
S-0.0561 Å °0.0778 Å °0.0416 Å °0.0591 Å °0.033 Å °-0.0516 Å °-0.0698 Å °-0.0468 Å °0.0243 Å °
Refinement TLS groupSelection details: all

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