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- PDB-5jvl: C4-type pyruvate phospate dikinase: nucleotide binding domain wit... -

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Basic information

Entry
Database: PDB / ID: 5jvl
TitleC4-type pyruvate phospate dikinase: nucleotide binding domain with bound ATP analogue
ComponentsPyruvate, phosphate dikinase, chloroplastic
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 / ATP-grasp fold, A domain / 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 / Dna Ligase; 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
Chem-6NQ / PHOSPHOENOLPYRUVATE / Pyruvate, phosphate dikinase, chloroplastic
Similarity search - Component
Biological speciesFlaveria trinervia (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 ...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
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_auth_seq_id / _struct_conn.ptnr2_label_asym_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
C: Pyruvate, phosphate dikinase, chloroplastic
D: Pyruvate, phosphate dikinase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)383,94518
Polymers381,3964
Non-polymers2,55014
Water00
1
A: Pyruvate, phosphate dikinase, chloroplastic
D: Pyruvate, phosphate dikinase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,26910
Polymers190,6982
Non-polymers1,5718
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-56 kcal/mol
Surface area67090 Å2
MethodPISA
2
B: Pyruvate, phosphate dikinase, chloroplastic
C: Pyruvate, phosphate dikinase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,6768
Polymers190,6982
Non-polymers9786
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-49 kcal/mol
Surface area54000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.980, 108.450, 152.760
Angle α, β, γ (deg.)106.220, 101.810, 98.320
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 95348.953 Da / Num. of mol.: 4
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-6NQ / 2'-Bromo-2'-deoxyadenosine 5'-[beta,gamma-imide]triphosphoric acid


Mass: 569.093 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16BrN6O11P3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5O6P

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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: 3.1 Å3/Da / Density % sol: 59.6 %
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, 0.75 mM 2'-Br-dAppNHp

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.919344 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2014
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919344 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 90103 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 37.38 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.097 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.9-33.90.4452.9198.7
3-3.123.90.3234.1198.6
3.12-3.263.90.2385.4198.8
3.26-3.443.90.177.3198.8
3.44-3.653.90.1239.9199
3.65-3.933.90.08713.3199.1
3.93-4.323.90.06217.4199
4.32-4.943.90.05320.1199
4.94-6.193.90.06317.4198.8
6.19-19.793.60.03926.1198.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.8 Å47.9 Å
Translation2.8 Å47.9 Å

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
PHASER2.5.7phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JVJ

5jvj


Resolution: 2.9→19.79 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.896 / Cross valid method: THROUGHOUT / ESU R Free: 0.352
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 1875 2.1 %RANDOM
Rwork0.2115 ---
obs0.2119 90103 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 139.3 Å2 / Biso mean: 46.8852 Å2 / Biso min: 10.79 Å2
Baniso -1Baniso -2Baniso -3
1--4.86 Å2-0.25 Å2-0.15 Å2
2--1.29 Å20.15 Å2
3---2.63 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23494 0 140 0 23634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01924059
X-RAY DIFFRACTIONr_bond_other_d00.0222938
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.97132589
X-RAY DIFFRACTIONr_angle_other_deg3.672352746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.29953122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02524.439998
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.824154048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.07515150
X-RAY DIFFRACTIONr_chiral_restr0.0810.23686
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02127493
X-RAY DIFFRACTIONr_gen_planes_other0.010.025226
X-RAY DIFFRACTIONr_mcbond_it0.5250.59412506
X-RAY DIFFRACTIONr_mcbond_other0.5250.59412505
X-RAY DIFFRACTIONr_mcangle_it0.9550.89115619
LS refinement shellResolution: 2.897→2.973 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 132 -
Rwork0.3 6377 -
all-6509 -
obs--96.02 %
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)
12.0280.0806-0.01942.88360.63422.013-0.0874-0.13470.4708-0.23040.08080.085-0.40040.03990.00670.76140.10760.04920.21780.03950.259.38813.065-58.032
24.57060.15120.4250.01590.04150.23280.1419-0.1204-0.05720.0178-0.04540.018-0.0238-0.1527-0.09650.7780.07270.12660.22060.00820.236836.043-10.213-68.998
31.058-1.4120.5962.8286-0.33651.06030.1111-0.10680.0054-0.1306-0.03250.28030.0408-0.3163-0.07860.87560.03010.10120.19550.0230.192725.237-28.601-67.105
40.60550.3973-0.29251.790.73622.4648-0.0095-0.01020.008-0.13510.00880.03490.1333-0.15010.00060.66860.05490.04730.08810.05220.036432.547-35.519-53.569
54.8489-2.1353.1557.4363-0.22492.72110.4523-0.0128-0.690.46340.0478-0.56370.82440.3579-0.50011.01340.1982-0.12880.33020.04260.375253.437-65.252-86.222
65.31631.7435-1.66151.1559-0.04742.0266-0.16241.0369-0.3917-0.23020.06330.39550.0628-0.54250.09911.32330.1134-0.00781.1205-0.230.748720.42-60.161-87.396
70.8491-0.41830.34132.44240.6842.80070.0346-0.092-0.13390.1346-0.05640.28950.1268-0.28560.02170.68350.02880.09120.09160.03570.064928.997-35.023-99.423
84.7235-2.5981-0.29673.18220.84771.1164-0.2093-0.7558-0.05420.76120.2886-0.1340.1660.0962-0.07941.08010.0165-0.10620.26790.0010.270315.30915.691-135.285
90.9880.6192-0.09351.1202-0.4780.4076-0.0275-0.338-0.18590.3907-0.0243-0.0505-0.044-0.02620.05180.82020.13280.03110.23690.04930.17298.487-14.487-144.416
102.8969-1.4717-0.34761.18490.14340.1698-0.1418-0.4315-0.27870.22930.15480.43240.1225-0.116-0.0130.9103-0.010.04230.34720.0180.23049.185-44.393-135.691
110.90540.00750.54982.19260.8822.87850.0493-0.1733-0.13460.1972-0.09990.15930.1533-0.16090.05060.5990.03460.11790.0430.03020.06624.968-45.49-130.926
121.160.63240.35021.66550.58621.0219-0.0440.4084-0.0694-0.30610.0362-0.090.05510.26760.00780.69060.09990.1060.25090.05960.148717.6-72.812-16.917
134.5721.55291.83041.02440.32710.9162-0.12370.6557-0.0240.05880.36120.3967-0.09290.1463-0.23750.69930.05130.16280.29380.0640.35656.46-32.947-22.838
141.4272-0.54610.21633.8608-0.55043.93250.14640.53640.1791-0.55990.01760.5921-0.1547-1.0912-0.16390.75210.10540.10640.5590.15510.251214.505-10.697-27.12
150.63360.1345-0.43772.07380.2342.15770.07130.07970.1657-0.0495-0.05220.1134-0.0452-0.1029-0.0190.56940.06320.07040.02970.03210.064827.664-22.24-27.703
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 325
2X-RAY DIFFRACTION2A326 - 485
3X-RAY DIFFRACTION3A486 - 646
4X-RAY DIFFRACTION4A646 - 874
5X-RAY DIFFRACTION5B256 - 384
6X-RAY DIFFRACTION6B390 - 508
7X-RAY DIFFRACTION7B509 - 874
8X-RAY DIFFRACTION8C1 - 240
9X-RAY DIFFRACTION9C241 - 480
10X-RAY DIFFRACTION10C481 - 640
11X-RAY DIFFRACTION11C641 - 874
12X-RAY DIFFRACTION12D1 - 400
13X-RAY DIFFRACTION13D401 - 560
14X-RAY DIFFRACTION14D561 - 640
15X-RAY DIFFRACTION15D641 - 874

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