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- PDB-9mdt: Crystal Structure Pyrophosphate-fructose 6-phosphate 1-phosphotra... -

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Basic information

Entry
Database: PDB / ID: 9mdt
TitleCrystal Structure Pyrophosphate-fructose 6-phosphate 1-phosphotransferase 1 (Pfk1) from Trichomonas vaginalis (ATP/Pyrophosphate complex)
ComponentsPyrophosphate--fructose 6-phosphate 1-phosphotransferase 1
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1 / Trichomonas vaginalis
Function / homology
Function and homology information


diphosphate-fructose-6-phosphate 1-phosphotransferase / diphosphate-fructose-6-phosphate 1-phosphotransferase activity / phosphofructokinase activity / 6-phosphofructokinase activity / fructose 6-phosphate metabolic process / response to glucose / metal ion binding / cytoplasm
Similarity search - Function
Pyrophosphate-dependent phosphofructokinase TM0289 type / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / PYROPHOSPHATE / Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure Pyrophosphate-fructose 6-phosphate 1-phosphotransferase 1 (Pfk1) from Trichomonas vaginalis (ATP/Pyrophosphate complex)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionDec 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1
B: Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1
C: Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1
D: Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,09227
Polymers190,5034
Non-polymers3,58923
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21510 Å2
ΔGint-167 kcal/mol
Surface area57670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.109, 87.109, 478.237
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Pyrophosphate--fructose 6-phosphate 1-phosphotransferase 1 / 6-phosphofructokinase / pyrophosphate dependent 1 / PPi-dependent phosphofructokinase 1 / PPi-PFK 1 ...6-phosphofructokinase / pyrophosphate dependent 1 / PPi-dependent phosphofructokinase 1 / PPi-PFK 1 / Pyrophosphate-dependent 6-phosphofructose-1-kinase 1


Mass: 47625.797 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: Pfk1, TVAG_430830 / Plasmid: TrvaA.00429.d.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O61068, diphosphate-fructose-6-phosphate 1-phosphotransferase

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Non-polymers , 6 types, 196 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus A4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2. TrvaA.00429.d.B1.PW39248 at 25 mg/mL. Overnight soak in 5 mM ...Details: Morpheus A4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2. TrvaA.00429.d.B1.PW39248 at 25 mg/mL. Overnight soak in 5 mM ATP and 5 mM Pyrophosphate. plate Liu-S-143 AB34. Puck: PSL-0309, Cryo: Direct

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Sep 28, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.16→49.29 Å / Num. obs: 100652 / % possible obs: 100 % / Redundancy: 26.3 % / CC1/2: 1 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.026 / Rrim(I) all: 0.133 / Χ2: 0.99 / Net I/σ(I): 21.8 / Num. measured all: 2652128
Reflection shellResolution: 2.16→2.22 Å / % possible obs: 100 % / Redundancy: 24.7 % / Rmerge(I) obs: 2.12 / Num. measured all: 180151 / Num. unique obs: 7293 / CC1/2: 0.371 / Rpim(I) all: 0.433 / Rrim(I) all: 2.164 / Χ2: 0.78 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIXdev_5508refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→48.74 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2292 4984 4.96 %
Rwork0.2016 --
obs0.2029 100458 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12871 0 199 173 13243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513294
X-RAY DIFFRACTIONf_angle_d0.60318023
X-RAY DIFFRACTIONf_dihedral_angle_d11.8094988
X-RAY DIFFRACTIONf_chiral_restr0.0462044
X-RAY DIFFRACTIONf_plane_restr0.0052292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.180.33621500.31183140X-RAY DIFFRACTION100
2.18-2.210.33991720.30373085X-RAY DIFFRACTION100
2.21-2.240.33211570.2933186X-RAY DIFFRACTION100
2.24-2.270.31561500.293085X-RAY DIFFRACTION100
2.27-2.30.3251830.27533151X-RAY DIFFRACTION100
2.3-2.330.27491630.26353098X-RAY DIFFRACTION100
2.33-2.360.32561930.24953109X-RAY DIFFRACTION100
2.36-2.40.27111620.25573112X-RAY DIFFRACTION100
2.4-2.430.33821400.25133156X-RAY DIFFRACTION100
2.43-2.470.28581600.24363152X-RAY DIFFRACTION100
2.47-2.520.27981690.24453134X-RAY DIFFRACTION100
2.52-2.560.27091570.24533179X-RAY DIFFRACTION100
2.56-2.610.27351860.23973069X-RAY DIFFRACTION100
2.61-2.660.26271780.23653155X-RAY DIFFRACTION100
2.66-2.720.28871750.22323159X-RAY DIFFRACTION100
2.72-2.780.27331390.2343153X-RAY DIFFRACTION100
2.78-2.850.2561670.22233152X-RAY DIFFRACTION100
2.85-2.930.25231790.21563167X-RAY DIFFRACTION100
2.93-3.020.25031860.21793143X-RAY DIFFRACTION100
3.02-3.120.27151590.24313190X-RAY DIFFRACTION100
3.12-3.230.29771390.23553214X-RAY DIFFRACTION100
3.23-3.360.27061610.20883192X-RAY DIFFRACTION100
3.36-3.510.21981560.20043191X-RAY DIFFRACTION100
3.51-3.690.21541700.18733192X-RAY DIFFRACTION100
3.69-3.920.19371630.17233229X-RAY DIFFRACTION100
3.92-4.230.20691850.15493231X-RAY DIFFRACTION100
4.23-4.650.15151660.14833241X-RAY DIFFRACTION100
4.65-5.320.17811750.16023282X-RAY DIFFRACTION100
5.33-6.710.20991710.19563368X-RAY DIFFRACTION100
6.71-48.740.20591730.19883559X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 42.1085 Å / Origin y: -1.7803 Å / Origin z: -31.4684 Å
111213212223313233
T0.2485 Å20.0451 Å2-0.0609 Å2-0.3265 Å20.0192 Å2--0.3676 Å2
L0.6483 °2-0.168 °2-0.1593 °2-0.6873 °2-0.0219 °2--1.6334 °2
S0.0064 Å °0.0586 Å °0.0695 Å °0.0075 Å °0.0637 Å °0.0374 Å °0.0649 Å °0.0782 Å °-0.0532 Å °
Refinement TLS groupSelection details: all

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