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- PDB-5jvj: C4-type pyruvate phosphate dikinase: different conformational sta... -

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Basic information

Entry
Database: PDB / ID: 5jvj
TitleC4-type pyruvate phosphate dikinase: different conformational states of the nucleotide binding domain in the dimer
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 / phosphorylation / ATP binding / metal ion binding
Similarity search - Function
Pyruvate Phosphate di-kinase; domain 2 / Pyruvate Phosphate Dikinase, domain 2 / Acyl-CoA Binding Protein - #30 / Pyruvate, phosphate dikinase / Pyruvate phosphate dikinase, AMP/ATP-binding / Pyruvate phosphate dikinase, AMP/ATP-binding domain / Phosphohistidine domain / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site ...Pyruvate Phosphate di-kinase; domain 2 / Pyruvate Phosphate Dikinase, domain 2 / Acyl-CoA Binding Protein - #30 / Pyruvate, phosphate dikinase / Pyruvate phosphate dikinase, AMP/ATP-binding / Pyruvate phosphate dikinase, AMP/ATP-binding domain / Phosphohistidine 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 / Acyl-CoA Binding Protein / Phosphoenolpyruvate-binding domains / Glucose Oxidase; domain 1 / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / D-amino Acid Aminotransferase; Chain A, domain 1 / 3-Layer(bba) Sandwich / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOENOLPYRUVATE / Pyruvate, phosphate dikinase, chloroplastic
Similarity search - Component
Biological speciesFlaveria trinervia (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.898 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)191,0836
Polymers190,6982
Non-polymers3854
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-42 kcal/mol
Surface area68060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.736, 69.044, 166.763
Angle α, β, γ (deg.)90.000, 112.840, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 380 or (resid 381 and (name...
21(chain B and (resid 380:642 or (resid 643 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPROPRO(chain A and (resid 380 or (resid 381 and (name...AA380380
12GLNGLNGLNGLN(chain A and (resid 380 or (resid 381 and (name...AA381381
13LYSLYSVALVAL(chain A and (resid 380 or (resid 381 and (name...AA1 - 8741 - 874
14LYSLYSVALVAL(chain A and (resid 380 or (resid 381 and (name...AA1 - 8741 - 874
15LYSLYSVALVAL(chain A and (resid 380 or (resid 381 and (name...AA1 - 8741 - 874
16LYSLYSVALVAL(chain A and (resid 380 or (resid 381 and (name...AA1 - 8741 - 874
21PROPROALAALA(chain B and (resid 380:642 or (resid 643 and (name...BB380 - 642380 - 642
22VALVALVALVAL(chain B and (resid 380:642 or (resid 643 and (name...BB643643
23LYSLYSVALVAL(chain B and (resid 380:642 or (resid 643 and (name...BB2 - 8742 - 874
24LYSLYSVALVAL(chain B and (resid 380:642 or (resid 643 and (name...BB2 - 8742 - 874
25LYSLYSVALVAL(chain B and (resid 380:642 or (resid 643 and (name...BB2 - 8742 - 874
26LYSLYSVALVAL(chain B and (resid 380:642 or (resid 643 and (name...BB2 - 8742 - 874

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Components

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


Mass: 95348.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flaveria trinervia (plant) / Gene: PPDK, PDK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22221, pyruvate, phosphate dikinase
#2: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE / Phosphoenolpyruvic acid


Mass: 168.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5O6P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / 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: 2.9 Å3/Da / Density % sol: 57.64 %
Crystal growTemperature: 294.15 K / Method: microbatch / pH: 7
Details: 0.1 M MOPS (pH 7.0), 0.1 M magnesium formiate, 17 % (w/v) PEG 3350, 10 mM phosphoenol pyruvate, 10 mM nicotinamide adenine dinucleotide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979938 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2014
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979938 Å / Relative weight: 1
ReflectionResolution: 2.898→49 Å / Num. obs: 48259 / % possible obs: 98.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 39.56 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.102 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.898-2.993.20.403197.8
11.59-492.70.034177.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49 Å
Translation2.5 Å49 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.25data scaling
PHASER2.5.6phasing
PHENIXdev_2386refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VBH

1vbh


Resolution: 2.898→38.421 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.01
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 1227 2.55 %RANDOM
Rwork0.2367 ---
obs0.2373 48150 98.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 161.08 Å2 / Biso mean: 59.1733 Å2 / Biso min: 9.23 Å2
Refinement stepCycle: final / Resolution: 2.898→38.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11919 0 22 0 11941
Biso mean--29.62 --
Num. residues----1662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212140
X-RAY DIFFRACTIONf_angle_d0.45916481
X-RAY DIFFRACTIONf_chiral_restr0.0411897
X-RAY DIFFRACTIONf_plane_restr0.0032194
X-RAY DIFFRACTIONf_dihedral_angle_d10.2777284
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5160X-RAY DIFFRACTION5.59TORSIONAL
12B5160X-RAY DIFFRACTION5.59TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8981-3.01410.31071270.29315152527998
3.0141-3.15120.31951440.28565198534299
3.1512-3.31720.32091450.27595207535299
3.3172-3.52490.30321280.26715218534699
3.5249-3.79690.2881450.24055260540599
3.7969-4.17860.20831270.20765218534599
4.1786-4.78220.22541230.19515287541099
4.7822-6.02140.26381470.23435290543799
6.0214-38.42440.21281410.21935093523493
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.9796-0.8945-0.27962.1739-0.66741.10350.17980.89560.0805-0.6735-0.30560.07110.10760.0230.01570.35860.0664-0.00550.22980.10150.336618.049270.861251.9064
20.54230.2065-0.04190.0786-0.01460.00310.15330.6618-0.4743-0.6058-0.2201-0.24950.50560.25810.0270.72570.30620.09390.4963-0.08340.425435.63654.657156.0729
30.250.28750.00150.3344-0.01750.12180.0058-0.007-0.0409-0.0223-0.0171-0.04840.02290.0082-0.0170.208-0.0179-0.0667-0.04-0.00220.295511.611959.353374.7807
40.35350.24560.02091.09510.27260.3605-0.00460.00930.01690.06860.00190.1375-0.0361-0.01750.01690.1688-0.0466-0.03420.03-0.01920.2597-13.813851.713870.6385
50.8751-0.04150.09190.9665-0.07460.6116-0.04190.0904-0.1839-0.05030.0195-0.04650.19370.01580.00390.19960.0234-0.00860.0198-0.03470.2048-33.976123.525363.0699
61.12210.2680.1010.53590.0491.0917-0.13530.3717-0.0203-0.10130.0895-0.08590.04990.29670.04350.1689-0.0415-0.0090.169-0.00490.1801-31.426930.726851.8231
70.540.4571-0.76251.186-0.49551.15050.20130.0366-0.00280.23750.00470.2328-0.30780.0977-0.16490.86350.33140.16641.76090.13290.6184-76.750427.63829.2049
80.75970.1474-0.81160.95630.23781.0443-0.00140.0609-0.0740.1998-0.00180.1865-0.0205-0.6449-0.02610.58270.15010.10031.58360.2280.6692-86.84985.78459.1066
90.41830.00920.1190.4855-0.170.0953-0.1773-0.0745-0.0219-0.18550.28280.2032-0.0627-0.461-0.1190.58030.0235-0.04131.69720.05180.4324-65.733915.7499-3.5333
100.55730.12720.86550.4755-0.21382.0636-0.00710.07430.0111-0.13350.0077-0.0040.19390.2218-0.10590.39360.1021-0.04611.3653-0.10340.3445-40.415522.64881.6839
110.206-0.07810.08070.21450.07670.0917-0.0292-0.1059-0.05470.07180.0831-0.12970.22910.4244-0.05990.41860.2161-0.03751.4173-0.22240.3421-11.161516.808320.2564
120.08770.0238-0.14710.19340.00410.37410.02310.26930.0171-0.1114-0.0702-0.180.06920.6095-0.00130.2596-0.00070.0291.2246-0.01210.2013-18.253527.084425.9032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resi 1:111 or resi 197:243)A0
2X-RAY DIFFRACTION2chain A and (resi 112:196)A1 - 874
3X-RAY DIFFRACTION3chain A and (resi 244:340)A1 - 874
4X-RAY DIFFRACTION4chain A and (resi 341:380 or resi 516:534)A1 - 874
5X-RAY DIFFRACTION4chain A and (resi 341:380 or resi 516:534)A1 - 874
6X-RAY DIFFRACTION5chain A and (resi 535:630)A1 - 874
7X-RAY DIFFRACTION6chain A and (resi 631:874)A1 - 874
8X-RAY DIFFRACTION7chain B and (resi 1:111 or resi 197:243)B0
9X-RAY DIFFRACTION8chain B and (resi 112:196)B2 - 874
10X-RAY DIFFRACTION9chain B and (resi 244:340)B2 - 874
11X-RAY DIFFRACTION10chain B and (resi 341:380 or resi 516:534)B2 - 874
12X-RAY DIFFRACTION10chain B and (resi 341:380 or resi 516:534)B2 - 874
13X-RAY DIFFRACTION11chain B and (resi 535:630)B2 - 874
14X-RAY DIFFRACTION12chain B and (resi 631:874)B2 - 874

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