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- PDB-6vr0: Agrobacterium Tumefaciens ADP-glucose pyrophosphorylase W106A -

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Basic information

Entry
Database: PDB / ID: 6vr0
TitleAgrobacterium Tumefaciens ADP-glucose pyrophosphorylase W106A
ComponentsGlucose-1-phosphate adenylyltransferase
KeywordsTRANSFERASE / ADP-Glc PPase / ADP-glucose pyrophosphorylase / enzyme / allosteric regulation
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. / : / 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 / Trimeric LpxA-like superfamily / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Glucose-1-phosphate adenylyltransferase / Glucose-1-phosphate adenylyltransferase
Similarity search - Component
Biological speciesRhizobium radiobacter (Agrobacterium genomosp. 4)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMascarenhas, R.N. / Liu, D. / Ballicora, M. / Iglesias, A. / Asencion, M. / Figueroa, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 1616851 United States
CitationJournal: To Be Published
Title: Agrobacterium Tumefaciens ADP-glucose pyrophosphorylase W106A
Authors: Mascarenhas, R.N. / Liu, D. / Ballicora, M. / Iglesias, A. / Asencion, M. / Figueroa, C. / Esper, M. / Aleanzi, M.
History
DepositionFeb 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)470,463100
Polymers461,82110
Non-polymers8,64290
Water7,674426
1
A: Glucose-1-phosphate adenylyltransferase
D: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,99719
Polymers92,3642
Non-polymers1,63317
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-229 kcal/mol
Surface area33660 Å2
MethodPISA
2
B: Glucose-1-phosphate adenylyltransferase
hetero molecules

B: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,32512
Polymers92,3642
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4950 Å2
ΔGint-182 kcal/mol
Surface area33610 Å2
MethodPISA
3
C: Glucose-1-phosphate adenylyltransferase
F: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,90118
Polymers92,3642
Non-polymers1,53716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-251 kcal/mol
Surface area33040 Å2
MethodPISA
4
E: Glucose-1-phosphate adenylyltransferase
hetero molecules

H: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,18921
Polymers92,3642
Non-polymers1,82519
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1/2,y-1/2,-z1
Buried area6330 Å2
ΔGint-261 kcal/mol
Surface area33660 Å2
MethodPISA
5
G: Glucose-1-phosphate adenylyltransferase
J: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,28522
Polymers92,3642
Non-polymers1,92120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-268 kcal/mol
Surface area33580 Å2
MethodPISA
6
I: Glucose-1-phosphate adenylyltransferase
hetero molecules

I: Glucose-1-phosphate adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,85428
Polymers92,3642
Non-polymers2,49026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7200 Å2
ΔGint-337 kcal/mol
Surface area33730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)433.318, 141.040, 92.510
Angle α, β, γ (deg.)90.000, 102.300, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-608-

HOH

21I-636-

HOH

31I-669-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 67 or (resid 68...
21(chain B and (resid 6 through 67 or (resid 68...
31(chain C and (resid 6 through 70 or (resid 71...
41(chain D and (resid 6 through 70 or (resid 71...
51(chain E and (resid 6 through 70 or (resid 71...
61(chain F and (resid 6 through 67 or (resid 68...
71(chain G and (resid 6 through 67 or (resid 68...
81(chain H and (resid 6 through 67 or (resid 68...
91(chain I and (resid 6 through 67 or (resid 68...
101(chain J and (resid 6 through 96 or resid 107 through 418 or resid 500 through 900))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 6 through 67 or (resid 68...A6 - 67
121(chain A and (resid 6 through 67 or (resid 68...A68
131(chain A and (resid 6 through 67 or (resid 68...A6 - 418
141(chain A and (resid 6 through 67 or (resid 68...A6 - 418
151(chain A and (resid 6 through 67 or (resid 68...A6 - 418
161(chain A and (resid 6 through 67 or (resid 68...A6 - 418
211(chain B and (resid 6 through 67 or (resid 68...B6 - 67
221(chain B and (resid 6 through 67 or (resid 68...B68
231(chain B and (resid 6 through 67 or (resid 68...B6 - 418
241(chain B and (resid 6 through 67 or (resid 68...B6 - 418
251(chain B and (resid 6 through 67 or (resid 68...B6 - 418
311(chain C and (resid 6 through 70 or (resid 71...C6 - 70
321(chain C and (resid 6 through 70 or (resid 71...C71
331(chain C and (resid 6 through 70 or (resid 71...C6 - 418
341(chain C and (resid 6 through 70 or (resid 71...C6 - 418
351(chain C and (resid 6 through 70 or (resid 71...C6 - 418
411(chain D and (resid 6 through 70 or (resid 71...D6 - 70
421(chain D and (resid 6 through 70 or (resid 71...D71
431(chain D and (resid 6 through 70 or (resid 71...D6 - 418
441(chain D and (resid 6 through 70 or (resid 71...D6 - 418
451(chain D and (resid 6 through 70 or (resid 71...D6 - 418
511(chain E and (resid 6 through 70 or (resid 71...E6 - 70
521(chain E and (resid 6 through 70 or (resid 71...E71
531(chain E and (resid 6 through 70 or (resid 71...E6 - 418
541(chain E and (resid 6 through 70 or (resid 71...E6 - 418
551(chain E and (resid 6 through 70 or (resid 71...E6 - 418
611(chain F and (resid 6 through 67 or (resid 68...F6 - 67
621(chain F and (resid 6 through 67 or (resid 68...F68
631(chain F and (resid 6 through 67 or (resid 68...F6 - 418
641(chain F and (resid 6 through 67 or (resid 68...F6 - 418
651(chain F and (resid 6 through 67 or (resid 68...F6 - 418
711(chain G and (resid 6 through 67 or (resid 68...G6 - 67
721(chain G and (resid 6 through 67 or (resid 68...G68
731(chain G and (resid 6 through 67 or (resid 68...G6 - 418
741(chain G and (resid 6 through 67 or (resid 68...G6 - 418
751(chain G and (resid 6 through 67 or (resid 68...G6 - 418
761(chain G and (resid 6 through 67 or (resid 68...G6 - 418
811(chain H and (resid 6 through 67 or (resid 68...H6 - 67
821(chain H and (resid 6 through 67 or (resid 68...H68
831(chain H and (resid 6 through 67 or (resid 68...H6 - 418
841(chain H and (resid 6 through 67 or (resid 68...H6 - 418
851(chain H and (resid 6 through 67 or (resid 68...H6 - 418
861(chain H and (resid 6 through 67 or (resid 68...H6 - 418
911(chain I and (resid 6 through 67 or (resid 68...I6 - 67
921(chain I and (resid 6 through 67 or (resid 68...I68
931(chain I and (resid 6 through 67 or (resid 68...I6 - 418
941(chain I and (resid 6 through 67 or (resid 68...I6 - 418
951(chain I and (resid 6 through 67 or (resid 68...I6 - 418
961(chain I and (resid 6 through 67 or (resid 68...I6 - 418
1011(chain J and (resid 6 through 96 or resid 107 through 418 or resid 500 through 900))J6 - 96
1021(chain J and (resid 6 through 96 or resid 107 through 418 or resid 500 through 900))J107 - 418
1031(chain J and (resid 6 through 96 or resid 107 through 418 or resid 500 through 900))J500 - 900

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Components

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


Mass: 46182.102 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (Agrobacterium genomosp. 4)
Gene: glgC, SY94_4053 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A083ZTG5, UniProt: P39669*PLUS, glucose-1-phosphate adenylyltransferase
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 89 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.05 Å3/Da / Density % sol: 59.62 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: 50mM HEPES pH 7.5 and 1.5 M Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: -h-2*l,-k,l / Fraction: 0.5
ReflectionResolution: 2.2→50.632 Å / Num. obs: 272607 / % possible obs: 99.3 % / Redundancy: 3.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.125 / Net I/σ(I): 4.5
Reflection shellResolution: 2.2→2.4 Å / Rmerge(I) obs: 0.948 / Num. unique obs: 13264 / CC1/2: 0.549

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W6J

5w6j


Resolution: 2.2→50.632 Å / Cross valid method: THROUGHOUT / σ(F): 104.57 / Phase error: 29.02
RfactorNum. reflection% reflection
Rfree0.2434 13608 5.02 %
Rwork0.2136 --
obs0.2305 272602 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.12 Å2 / Biso mean: 30.2135 Å2 / Biso min: 8.77 Å2
Refinement stepCycle: final / Resolution: 2.2→50.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31704 0 451 426 32581
Biso mean--39 23.4 -
Num. residues----4040
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A12290X-RAY DIFFRACTION3.863TORSIONAL
12B12290X-RAY DIFFRACTION3.863TORSIONAL
13C12290X-RAY DIFFRACTION3.863TORSIONAL
14D12290X-RAY DIFFRACTION3.863TORSIONAL
15E12290X-RAY DIFFRACTION3.863TORSIONAL
16F12290X-RAY DIFFRACTION3.863TORSIONAL
17G12290X-RAY DIFFRACTION3.863TORSIONAL
18H12290X-RAY DIFFRACTION3.863TORSIONAL
19I12290X-RAY DIFFRACTION3.863TORSIONAL
110J12290X-RAY DIFFRACTION3.863TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.23810.30676740.2693126771335193
2.2381-2.27880.29366180.2651127731339193
2.2788-2.32260.30796480.2679127581340693
2.3226-2.370.29877070.2758127801348793
2.37-2.42150.31866970.2772127801347793
2.4215-2.47790.32536830.2731128851356894
2.4779-2.53980.32756990.2697127511345094
2.5398-2.60850.29817060.2698129281363494
2.6085-2.68530.31166310.2707129911362295
2.6853-2.77190.32956820.2688129721365494
2.7719-2.8710.29727020.2607128791358194
2.871-2.98590.29176720.2552129911366395
2.9859-3.12180.27897140.2478130221373695
3.1218-3.28630.26166420.2432130731371595
3.2863-3.49210.26837010.2268129691367095
3.4921-3.76170.25546880.2094130401372895
3.7617-4.140.20576640.1902131691383395
4.14-4.73850.18026950.1684130591375495
4.7385-5.96810.20797240.1953131371386195
5.9681-46.26510.21716600.208133001396095

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