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

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Basic information

Entry
Database: PDB / ID: 9med
TitleCrystal Structure Pyrophosphate-fructose 6-phosphate 1-phosphotransferase 1 (Pfk1) from Trichomonas vaginalis (AMP/beta-D-Glucose-6-phosphate 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 / 6-O-phosphono-beta-D-glucopyranose / 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: 2.62 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 (AMP/beta-D-Glucose-6-phosphate complex)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionDec 6, 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

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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)193,50522
Polymers190,5034
Non-polymers3,00218
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20990 Å2
ΔGint-99 kcal/mol
Surface area58340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.875, 86.875, 475.979
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 / Sugars , 2 types, 6 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
#6: Sugar ChemComp-BG6 / 6-O-phosphono-beta-D-glucopyranose / BETA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 32 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
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. 5 hour soak in 2 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. 5 hour soak in 2 mM AMP and beta-D-Glucose-6-phosphate in crystallant. plate Liu-S-143 AB34. Puck: PSL-0415, 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: 2.62→49.09 Å / Num. obs: 56602 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.028 / Rrim(I) all: 0.103 / Χ2: 1.08 / Net I/σ(I): 21.8 / Num. measured all: 732317
Reflection shellResolution: 2.62→2.69 Å / % possible obs: 100 % / Redundancy: 13.8 % / Rmerge(I) obs: 1.384 / Num. measured all: 56331 / Num. unique obs: 4077 / CC1/2: 0.558 / Rpim(I) all: 0.385 / Rrim(I) all: 1.437 / Χ2: 0.8 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIXdev_5508refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→48.57 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2342 2768 4.9 %
Rwork0.1923 --
obs0.1944 56452 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.62→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12863 0 180 16 13059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313278
X-RAY DIFFRACTIONf_angle_d0.64917993
X-RAY DIFFRACTIONf_dihedral_angle_d12.6364940
X-RAY DIFFRACTIONf_chiral_restr0.0432054
X-RAY DIFFRACTIONf_plane_restr0.0052291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.670.32431410.27582617X-RAY DIFFRACTION100
2.67-2.710.31961260.26082654X-RAY DIFFRACTION100
2.71-2.770.30971120.25542601X-RAY DIFFRACTION100
2.77-2.820.29661350.24832658X-RAY DIFFRACTION100
2.82-2.880.30831320.24582621X-RAY DIFFRACTION100
2.88-2.950.32371510.23492613X-RAY DIFFRACTION100
2.95-3.020.28011250.24882654X-RAY DIFFRACTION100
3.02-3.110.32461730.26352627X-RAY DIFFRACTION100
3.11-3.20.3291200.26142645X-RAY DIFFRACTION100
3.2-3.30.28391380.24112653X-RAY DIFFRACTION100
3.3-3.420.2451250.20892666X-RAY DIFFRACTION100
3.42-3.560.2441570.19542629X-RAY DIFFRACTION100
3.56-3.720.26191390.1882680X-RAY DIFFRACTION100
3.72-3.910.20261320.18252693X-RAY DIFFRACTION100
3.91-4.160.20421140.15812730X-RAY DIFFRACTION100
4.16-4.480.17121470.14752681X-RAY DIFFRACTION100
4.48-4.930.181270.14892739X-RAY DIFFRACTION100
4.93-5.640.22261680.17982718X-RAY DIFFRACTION100
5.64-7.10.24531520.20072796X-RAY DIFFRACTION100
7.11-48.570.20781540.18163009X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 42.0304 Å / Origin y: -2.0802 Å / Origin z: -31.3844 Å
111213212223313233
T0.321 Å20.0554 Å2-0.0875 Å2-0.452 Å20.0083 Å2--0.467 Å2
L0.619 °2-0.1536 °2-0.16 °2-0.9204 °2-0.0905 °2--1.9296 °2
S-0.0317 Å °0.0601 Å °0.1023 Å °0.0183 Å °0.1357 Å °0.048 Å °0.0377 Å °0.0099 Å °-0.0719 Å °
Refinement TLS groupSelection details: all

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