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- PDB-5jvn: C3-type pyruvate phosphate dikinase: intermediate state of the ce... -

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Basic information

Entry
Database: PDB / ID: 5jvn
TitleC3-type pyruvate phosphate dikinase: intermediate state of the central domain in the swiveling mechanism
ComponentsPyruvate, phosphate dikinase, chloroplasticPyruvic acid
KeywordsTRANSFERASE / phosphotransferase / nucleotide binding / conformational transition / swiveling mechanism
Function / homology
Function and homology information


pyruvate, phosphate dikinase / pyruvate, phosphate dikinase activity / pyruvate metabolic process / photosynthesis / chloroplast / kinase activity / ATP binding / metal ion binding
Similarity search - Function
Pyruvate, phosphate dikinase / Pyruvate phosphate dikinase, AMP/ATP-binding / Pyruvate phosphate dikinase, AMP/ATP-binding domain / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site / PEP-utilizing enzymes signature 2. / PEP-utilising enzyme, C-terminal / PEP-utilising enzyme, PEP-binding domain / PEP-utilising enzyme, mobile domain ...Pyruvate, phosphate dikinase / Pyruvate phosphate dikinase, AMP/ATP-binding / Pyruvate phosphate dikinase, AMP/ATP-binding domain / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site / PEP-utilizing enzymes signature 2. / PEP-utilising enzyme, C-terminal / PEP-utilising enzyme, PEP-binding domain / PEP-utilising enzyme, mobile domain / Phosphohistidine domain superfamily / PEP-utilising enzyme, mobile domain / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / ATP-grasp fold, subdomain 1
Similarity search - Domain/homology
Chem-6NQ / PHOSPHOENOLPYRUVATE / Pyruvate, phosphate dikinase, chloroplastic
Similarity search - Component
Biological speciesFlaveria pringlei (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMinges, A. / Hoeppner, A. / Groth, G.
CitationJournal: Sci Rep / Year: 2017
Title: Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase.
Authors: Minges, A. / Ciupka, D. / Winkler, C. / Hoppner, A. / Gohlke, H. / Groth, G.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Jan 10, 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

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Assembly

Deposited unit
A: Pyruvate, phosphate dikinase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3304
Polymers95,5681
Non-polymers7613
Water0
1
A: Pyruvate, phosphate dikinase, chloroplastic
hetero molecules

A: Pyruvate, phosphate dikinase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,6608
Polymers191,1372
Non-polymers1,5236
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_674x-y+1,-y+2,-z-11
Buried area5110 Å2
ΔGint-41 kcal/mol
Surface area69980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)249.430, 249.430, 84.060
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Pyruvate, phosphate dikinase, chloroplastic / Pyruvic acid / Pyruvate / orthophosphate dikinase


Mass: 95568.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flaveria pringlei (plant) / Gene: PPDK, PDK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q42736, pyruvate, phosphate dikinase
#2: Chemical ChemComp-6NQ / 2'-Bromo-2'-deoxyadenosine 5'-[beta,gamma-imide]triphosphoric acid


Mass: 569.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16BrN6O11P3
#3: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE / Phosphoenolpyruvic acid


Mass: 168.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5O6P
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 4 Å3/Da / Density % sol: 68.6 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 17 % (w/v) PEG 4000, 15 % (w/v) glycerol, 85 mM HEPES (pH 7.5), 5 % (v/v) isopropanol, 10 mM phosphoenol pyruvate, 2.5 mM magnesium sulfate, 1 mM 2'-Br-dAppNHp

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976252 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 8, 2015 / Details: Toroidal mirror
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976252 Å / Relative weight: 1
ReflectionResolution: 2.9→49.54 Å / Num. obs: 34537 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 65.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.9-3.046.80.5972.71100
9.62-49.545.70.05135.8199.1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.25data scaling
PHASER2.6.0phasing
BUCCANEER1.6.0model building
REFMAC5.8.0135refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JVL
Resolution: 2.9→49.54 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.582 / ESU R Free: 0.31
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 1695 4.9 %RANDOM
Rwork0.1978 ---
obs0.1996 34536 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 191.03 Å2 / Biso mean: 90.5836 Å2 / Biso min: 48.59 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20.84 Å20 Å2
2--1.68 Å2-0 Å2
3----5.44 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6496 0 42 0 6538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196677
X-RAY DIFFRACTIONr_bond_other_d00.026309
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.979059
X-RAY DIFFRACTIONr_angle_other_deg3.682314488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7885875
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86124.396273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07151092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8351541
X-RAY DIFFRACTIONr_chiral_restr0.0540.21026
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217680
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021456
X-RAY DIFFRACTIONr_mcbond_it1.9334.8723500
X-RAY DIFFRACTIONr_mcbond_other1.934.8713499
X-RAY DIFFRACTIONr_mcangle_it3.0847.3114375
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 113 -
Rwork0.304 2380 -
all-2493 -
obs--99.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.7121-0.5198-0.66015.49380.19415.26970.1-0.05580.42560.2987-0.1136-0.0721-0.2696-0.00530.01370.1964-0.0489-0.02030.2614-0.0220.11691.457169.417-63.931
24.248-2.451-0.50914.1150.72333.9943-0.2701-0.52430.39480.60270.2856-0.435-0.00360.4628-0.01560.3059-0.0814-0.02350.2322-0.05810.063618.2160.062-58.438
30.92260.64930.258616.09610.55710.7896-0.0150.0703-0.1541-0.1275-0.0076-0.3214-0.01340.14010.02260.30780.03860.05250.21530.01290.043717.524180.783-81.431
44.6878-1.51791.83111.3164-1.67743.8110.2219-0.0966-0.0359-0.5-0.3161-0.52871.05391.75950.09430.97530.40460.03871.2385-0.24110.585642.473193.834-68.184
51.22641.4443-0.09424.16280.8273.15480.0848-0.2888-0.10940.1434-0.1223-0.6606-0.16911.00930.03760.50050.02990.00490.45570.07020.14836.901224.985-65.489
60.21430.2605-0.11432.5898-0.44862.79950.0111-0.09040.02470.1337-0.1501-0.2641-0.17890.42470.13910.3914-0.0043-0.01430.30270.03110.047730.243222.596-54.956
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 107
2X-RAY DIFFRACTION1A875
3X-RAY DIFFRACTION2A108 - 246
4X-RAY DIFFRACTION3A247 - 369
5X-RAY DIFFRACTION4A370 - 522
6X-RAY DIFFRACTION5A523 - 631
7X-RAY DIFFRACTION6A632 - 874

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