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- PDB-5w5r: Agrobacterium tumefaciens ADP-glucose pyrophosphorylase P96A muta... -

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Basic information

Entry
Database: PDB / ID: 5w5r
TitleAgrobacterium tumefaciens ADP-glucose pyrophosphorylase P96A mutant bound to activator pyruvate
ComponentsGlucose-1-phosphate adenylyltransferase
KeywordsTRANSFERASE / Glucose-1-phosphate adenylyltransferase / glycogen biosynthesis / starch biosynthesis / allosterism
Function / homology
Function and homology information


glucose-1-phosphate adenylyltransferase / glucose-1-phosphate adenylyltransferase activity / glycogen biosynthetic process / ATP 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
PYRUVIC ACID / Glucose-1-phosphate adenylyltransferase
Similarity search - Component
Biological speciesRhizobium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.754 Å
AuthorsMascarenhas, R.N. / Hill, B.L. / Ballicora, M.A. / Liu, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1616851 United States
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Structural analysis reveals a pyruvate-binding activator site in theAgrobacterium tumefaciensADP-glucose pyrophosphorylase.
Authors: Hill, B.L. / Mascarenhas, R. / Patel, H.P. / Asencion Diez, M.D. / Wu, R. / Iglesias, A.A. / Liu, D. / Ballicora, M.A.
History
DepositionJun 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _pdbx_audit_support.funding_organization
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_atom_id_1

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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
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
N: Glucose-1-phosphate adenylyltransferase
O: Glucose-1-phosphate adenylyltransferase
P: Glucose-1-phosphate adenylyltransferase
Q: Glucose-1-phosphate adenylyltransferase
R: Glucose-1-phosphate adenylyltransferase
F: Glucose-1-phosphate adenylyltransferase
G: Glucose-1-phosphate adenylyltransferase
M: Glucose-1-phosphate adenylyltransferase
T: Glucose-1-phosphate adenylyltransferase
U: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)937,91971
Polymers933,09220
Non-polymers4,82751
Water139,0047716
1
A: Glucose-1-phosphate adenylyltransferase
E: Glucose-1-phosphate adenylyltransferase
P: Glucose-1-phosphate adenylyltransferase
hetero molecules

O: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,65915
Polymers186,6184
Non-polymers1,04111
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_654x+1,y,z-11
Buried area14370 Å2
ΔGint-158 kcal/mol
Surface area62080 Å2
MethodPISA
2
B: Glucose-1-phosphate adenylyltransferase
D: Glucose-1-phosphate adenylyltransferase
K: Glucose-1-phosphate adenylyltransferase
M: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,56314
Polymers186,6184
Non-polymers94510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14670 Å2
ΔGint-144 kcal/mol
Surface area62430 Å2
MethodPISA
3
C: Glucose-1-phosphate adenylyltransferase
H: Glucose-1-phosphate adenylyltransferase
I: Glucose-1-phosphate adenylyltransferase
G: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,56314
Polymers186,6184
Non-polymers94510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14560 Å2
ΔGint-149 kcal/mol
Surface area61970 Å2
MethodPISA
4
L: Glucose-1-phosphate adenylyltransferase
R: Glucose-1-phosphate adenylyltransferase
hetero molecules

J: Glucose-1-phosphate adenylyltransferase
hetero molecules

N: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,47513
Polymers186,6184
Non-polymers8579
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_564x,y+1,z-11
crystal symmetry operation1_664x+1,y+1,z-11
Buried area14190 Å2
ΔGint-155 kcal/mol
Surface area62940 Å2
MethodPISA
5
Q: Glucose-1-phosphate adenylyltransferase
F: Glucose-1-phosphate adenylyltransferase
T: Glucose-1-phosphate adenylyltransferase
U: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,65915
Polymers186,6184
Non-polymers1,04111
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14650 Å2
ΔGint-157 kcal/mol
Surface area62540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.400, 140.993, 228.209
Angle α, β, γ (deg.)72.000, 78.180, 90.010
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 46654.590 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Gene: glgC / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: P39669, glucose-1-phosphate adenylyltransferase
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H4O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7716 / Source method: isolated from a natural source / Formula: H2O

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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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 50 mM Hepes, 1.5 M lithium sulfate at pH 7.5

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Reflection twinOperator: h,-k,h-l / Fraction: 0.49
ReflectionResolution: 1.75→50 Å / Num. obs: 1029422 / % possible obs: 95.4 % / Redundancy: 2 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.066 / Rrim(I) all: 0.093 / Χ2: 0.874 / Net I/σ(I): 8.4 / Num. measured all: 2012923
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.7820.547516500.6720.5440.7720.68295.8
1.78-1.8120.436517220.7470.4350.6160.70896
1.81-1.8520.36519320.8210.3580.5080.71896.2
1.85-1.8920.307518920.8730.3060.4330.7496.2
1.89-1.9320.247521230.8940.2460.3480.79196.4
1.93-1.9720.212520680.9170.2110.30.81796.6
1.97-2.0220.167521350.9410.1670.2360.85596.6
2.02-2.0720.144522090.9570.1440.2040.87596.7
2.07-2.1420.129522010.9630.1280.1820.91796.8
2.14-2.220.112522710.9730.1120.1580.96696.7
2.2-2.2820.1520590.9750.10.1411.00496.5
2.28-2.3820.09522270.980.0890.1271.02696.7
2.38-2.4820.083521570.980.0830.1181.0496.7
2.48-2.6120.076520800.9820.0750.1071.05496.5
2.61-2.7820.069520210.9850.0690.0981.06196.4
2.78-2.9920.061518240.9880.0610.0871.07895.9
2.99-3.2920.055510680.9880.0550.0781.04494.7
3.29-3.771.90.051507790.9880.0510.0720.94794.2
3.77-4.751.90.04486360.9910.040.0570.6590.1
4.75-501.90.031463680.9950.0310.0440.40785.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data scaling
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.754→46.884 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.07 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.228 2172 0.23 %
Rwork0.2008 950644 -
obs0.2022 953316 43.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.5 Å2 / Biso mean: 26.5494 Å2 / Biso min: 7.09 Å2
Refinement stepCycle: final / Resolution: 1.754→46.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms64444 0 264 7716 72424
Biso mean--25.42 33.03 -
Num. residues----8229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00466296
X-RAY DIFFRACTIONf_angle_d0.80190113
X-RAY DIFFRACTIONf_chiral_restr0.039814
X-RAY DIFFRACTIONf_plane_restr0.00411819
X-RAY DIFFRACTIONf_dihedral_angle_d13.04424112
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.754-1.80.3544890.2975400684015726
1.8-1.84870.33821080.2805501355024333
1.8487-1.90310.25681290.2698608296095839
1.9031-1.96450.31721500.2568693966954645
1.9645-2.03470.26821500.2473739357408548
2.0347-2.11610.21881580.2413742627442048
2.1161-2.21240.23791550.2383744177457248
2.2124-2.32910.25421610.2243743127447348
2.3291-2.47490.231610.2208742027436348
2.4749-2.6660.23091560.2147741967435248
2.666-2.93410.20421550.2737947394948
2.9341-3.35840.24391500.1786728327298247
3.3584-4.22990.19651480.144714017154946
4.2299-34.1080.20111420.1836668656700743

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