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- PDB-2x0s: 3.0 A RESOLUTION CRYSTAL STRUCTURE OF GLYCOSOMAL PYRUVATE PHOSPHA... -

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Basic information

Entry
Database: PDB / ID: 2x0s
Title3.0 A RESOLUTION CRYSTAL STRUCTURE OF GLYCOSOMAL PYRUVATE PHOSPHATE DIKINASE FROM TRYPANOSOMA BRUCEI
ComponentsPYRUVATE PHOSPHATE DIKINASE
KeywordsTRANSFERASE / KINASE / TROPICAL PARASITE
Function / homology
Function and homology information


pyruvate, phosphate dikinase / pyruvate, phosphate dikinase activity / glycosome / pyruvate metabolic process / phosphorylation / phosphate ion binding / kinase activity / 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, C-terminal ...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, 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, subdomain 1 / ATP-grasp fold, B domain / 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
Pyruvate, phosphate dikinase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.997 Å
AuthorsCosenza, L.W. / Bringaud, F. / Baltz, T. / Vellieux, F.M.D.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: The 3.0 A Resolution Crystal Structure of Glycosomal Pyruvate Phosphate Dikinase from Trypanosoma Brucei
Authors: Cosenza, L.W. / Bringaud, F. / Baltz, T. / Vellieux, F.M.D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary Crystallographic Investigation of Glycosomal Pyruvate Phosphate Dikinase from Trypanosoma Brucei
Authors: Cosenza, L.W. / Bringaud, F. / Baltz, T. / Vellieux, F.M.D.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Functional and Molecular Characterization of a Glycosomal Ppi-Dependent Enzyme in Trypanosomatids: Pyruvate, Phosphate Dikinase
Authors: Bringaud, F. / Baltz, D. / Baltz, T.
History
DepositionDec 17, 2009Deposition site: PDBE / Processing site: PDBE
SupersessionDec 29, 2009ID: 1H6Z
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ... DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PYRUVATE PHOSPHATE DIKINASE


Theoretical massNumber of molelcules
Total (without water)100,5451
Polymers100,5451
Non-polymers00
Water64936
1
A: PYRUVATE PHOSPHATE DIKINASE

A: PYRUVATE PHOSPHATE DIKINASE


Theoretical massNumber of molelcules
Total (without water)201,0902
Polymers201,0902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4000 Å2
ΔGint-21.82 kcal/mol
Surface area76810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.170, 153.500, 65.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PYRUVATE PHOSPHATE DIKINASE


Mass: 100544.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Strain: ANTAT1 / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O76283, pyruvate, phosphate dikinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 5

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.8
Details: HANGING DROP, 2 MICROLITER PROTEIN AND 2 MICROLITER PRECIPITANT SOLUTION. PROTEIN SOLUTION. 50 MG/ML, 20 MM IMIDAZOLE PH 7.0, 100 MM NACL, 100 MM MGCL2, 20% (V/V) GLYCEROL. PRECIPITANT ...Details: HANGING DROP, 2 MICROLITER PROTEIN AND 2 MICROLITER PRECIPITANT SOLUTION. PROTEIN SOLUTION. 50 MG/ML, 20 MM IMIDAZOLE PH 7.0, 100 MM NACL, 100 MM MGCL2, 20% (V/V) GLYCEROL. PRECIPITANT SOLUTION. 0.1 M BICINE PH 8.8, 1.5 % (W/V) PEG 5000 MONOMETHYLETHER, 10 % (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.964
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 3→24 Å / Num. obs: 24120 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 61 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.8
Reflection shellResolution: 3→3.1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.1 / % possible all: 88.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
BIOMOLSCALKB2 KBAPLY CCP4 TRUNCATEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DIK

1dik


Resolution: 2.997→23.938 Å / SU ML: 0.35 / σ(F): 1.62 / Phase error: 23.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2415 1163 4.8 %
Rwork0.1649 --
obs0.1687 24115 95.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.101 Å2 / ksol: 0.253 e/Å3
Displacement parametersBiso mean: 81.08 Å2
Baniso -1Baniso -2Baniso -3
1-6.1816 Å2-0 Å2-0 Å2
2---1.6729 Å20 Å2
3----4.8838 Å2
Refinement stepCycle: LAST / Resolution: 2.997→23.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6935 0 0 36 6971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097077
X-RAY DIFFRACTIONf_angle_d1.3459543
X-RAY DIFFRACTIONf_dihedral_angle_d21.4232655
X-RAY DIFFRACTIONf_chiral_restr0.0821045
X-RAY DIFFRACTIONf_plane_restr0.0061258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9971-3.13320.35911250.29792548X-RAY DIFFRACTION87
3.1332-3.2980.3311300.26462741X-RAY DIFFRACTION92
3.298-3.5040.34661580.2142803X-RAY DIFFRACTION95
3.504-3.77360.27591390.182889X-RAY DIFFRACTION98
3.7736-4.15160.24871590.1542931X-RAY DIFFRACTION98
4.1516-4.74830.20221720.12532924X-RAY DIFFRACTION99
4.7483-5.9670.20531400.13733005X-RAY DIFFRACTION99
5.967-23.93830.17521400.12863111X-RAY DIFFRACTION98
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)
12.7338-0.8032-0.02491.726-0.05721.0671-0.5428-0.7624-0.26170.23120.0925-0.14330.0192-0.04080.3391-0.0040.1316-0.04750.1716-0.01320.1719-15.238847.956743.5576
20.9601-0.59360.16870.9597-0.91552.0306-0.22390.1209-0.08370.05150.1106-0.0284-0.0066-0.46670.02030.14050.1068-0.12660.1713-0.05220.1664-25.645158.025623.1497
30.8135-0.74030.14791.02130.00540.9054-0.0888-0.04750.0567-0.06970.0507-0.0888-0.07940.07680.06180.0529-0.0051-0.11020.0124-0.00810.14582.172852.957823.7309
41.3774-0.33260.57481.9031-0.3161.91360.40860.2024-0.0873-0.9045-0.3080.2890.1142-0.0275-0.08160.29720.1718-0.34050.27590.1129-0.10855.093445.6315-0.183
50.94680.4012-0.0521.248-0.10790.0059-0.87690.3206-0.0536-0.40230.3842-0.39880.2144-0.2390.23360.4826-0.48350.52740.0353-0.16380.131823.58359.6195.1942
61.31441.0504-0.43481.6275-0.16650.202-0.80690.4343-0.4477-1.19880.5441-0.49650.1102-0.22830.16980.6192-0.48930.34850.1554-0.16750.227617.401-1.46056.0768
71.67790.89160.191.5182-0.74160.6763-0.2054-0.2323-0.0053-0.34450.24140.01970.1572-0.1375-0.07850.0485-0.05-0.04130.12430.01140.11148.217415.219622.1166
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:73)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 74:218)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 219:401)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 402:545)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 546:652)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 653:812)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 813:903)

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