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- PDB-5lu4: C4-type pyruvate phosphate dikinase: conformational intermediate ... -

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Basic information

Entry
Database: PDB / ID: 5lu4
TitleC4-type pyruvate phosphate dikinase: conformational intermediate of central domain in the swiveling mechanism
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 / 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
ADENOSINE-5'-DIPHOSPHATE / PYRUVIC ACID / Pyruvate, phosphate dikinase, chloroplastic
Similarity search - Component
Biological speciesFlaveria trinervia (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMinges, A. / Hoeppner, A. / Groth, G.
CitationJournal: Protein Sci. / Year: 2017
Title: Trapped intermediate state of plant pyruvate phosphate dikinase indicates substeps in catalytic swiveling domain mechanism.
Authors: Minges, A. / Hoppner, A. / Groth, G.
History
DepositionSep 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_struct_conn_angle.ptnr3_label_atom_id / _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
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)191,7389
Polymers190,6982
Non-polymers1,0407
Water362
1
A: Pyruvate, phosphate dikinase, chloroplastic
hetero molecules

B: Pyruvate, phosphate dikinase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,7389
Polymers190,6982
Non-polymers1,0407
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_995-x+9/2,-y+4,z+1/21
2
B: Pyruvate, phosphate dikinase, chloroplastic
hetero molecules

A: Pyruvate, phosphate dikinase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,7389
Polymers190,6982
Non-polymers1,0407
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_994-x+9/2,-y+4,z-1/21
Unit cell
Length a, b, c (Å)74.159, 126.515, 218.998
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 95348.953 Da / Num. of mol.: 2 / Fragment: UNP residues 80-953
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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.8 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES (pH 6.5), 0.3 M MgCl2, 10% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 24, 2016 / Details: KB mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.9→219 Å / Num. obs: 46486 / % possible obs: 99.8 % / Redundancy: 4.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Net I/σ(I): 20.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.9-35.20.4990.871199.7
11.23-2193.70.0210.998198.6

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASER2.6.1phasing
BUCCANEER1.6.1model building
REFMAC5.8.0155refinement
PHENIXdev_2499refinement
PDB_EXTRACT3.21data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JVL

5jvl


Resolution: 2.9→109.79 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.9 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.441
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 2229 4.8 %RANDOM
Rwork0.2474 ---
obs0.2492 46418 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 236.04 Å2 / Biso mean: 99.0676 Å2 / Biso min: 18.92 Å2
Baniso -1Baniso -2Baniso -3
1-4.41 Å20 Å20 Å2
2---0.64 Å20 Å2
3----3.77 Å2
Refinement stepCycle: LAST / Resolution: 2.9→109.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11954 0 64 2 12020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01912237
X-RAY DIFFRACTIONr_bond_other_d00.0210941
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.96616686
X-RAY DIFFRACTIONr_angle_other_deg3.933324968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.61651693
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.41324.342456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.319151677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2511562
X-RAY DIFFRACTIONr_chiral_restr0.0820.21918
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114504
X-RAY DIFFRACTIONr_gen_planes_other0.0120.022708
X-RAY DIFFRACTIONr_mcbond_it0.3070.6886784
X-RAY DIFFRACTIONr_mcbond_other0.3070.6886783
X-RAY DIFFRACTIONr_mcangle_it0.5531.0328473
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 173 -
Rwork0.357 3221 -
all-3394 -
obs--99.44 %
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)
12.08370.57930.21747.21360.88423.4562-0.03890.10790.2609-0.54140.10750.6007-0.2454-0.3265-0.06850.5063-0.076-0.01231.17410.06851.2964140.232244.59207.982
20.99170.6049-1.04631.76780.2332.9482-0.04390.03170.0518-0.34180.2799-0.09640.39480.31-0.2360.40220.0622-0.10231.1613-0.12850.9991171.155238.498192.562
33.29711.9636-4.15219.129-3.84546.27150.1878-0.21240.70890.7024-0.1988-2.0396-0.391.56830.0110.788-0.012-0.03492.4010.35731.7352186.133237.317156.35
42.6872-0.78471.15253.1636-2.48793.68960.15170.28110.1533-0.2752-0.2174-0.61620.3810.62150.06570.89890.1190.10161.166-0.09790.9194170.207232.45158.439
53.272-1.25870.44513.44671.15153.047-0.02380.1935-0.0747-0.20520.09630.01180.0302-0.0895-0.07260.0285-0.08090.04340.8475-0.11130.7422172.043275.865208.692
61.72311.62060.29883.6324-0.72220.76940.4628-0.5341-0.02540.529-0.11580.23570.4448-0.0134-0.3470.90.2355-0.11231.4113-0.27141.1514178.998245.311236.24
73.28953.7582-4.20569.0748-8.6868.6598-0.2334-0.0122-2.1319-0.8757-0.7617-0.45231.31560.52920.99522.6450.462-0.471.3637-0.04622.3385186.905238.211262.995
82.4861-0.5617-1.90281.86061.08095.48760.0371-0.2131-0.7790.3170.1277-0.04980.70460.471-0.16480.88040.1427-0.16191.10350.03421.0853186.037255.353260.894
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 243
2X-RAY DIFFRACTION2B244 - 555
3X-RAY DIFFRACTION3B556 - 634
4X-RAY DIFFRACTION4B635 - 872
5X-RAY DIFFRACTION5A1 - 337
6X-RAY DIFFRACTION6A338 - 554
7X-RAY DIFFRACTION7A555 - 617
8X-RAY DIFFRACTION8A618 - 872

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