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- PDB-8dop: Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate en... -

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Basic information

Entry
Database: PDB / ID: 8dop
TitleCrystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from Klebsiella aerogenes (P1 Form)
Components2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase
KeywordsISOMERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process
Similarity search - Function
Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesKlebsiella aerogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSeattle 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)HHSN272201700059C United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from Klebsiella aerogenes (P1 Form)
Authors: Lovell, S. / Liu, L. / Seibold, S. / Battaile, K.P.
History
DepositionJul 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / diffrn / Item: _diffrn.ambient_temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase
B: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase
C: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase
D: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase
E: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase
F: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase
G: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase
H: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,34426
Polymers218,6838
Non-polymers1,66118
Water7,026390
1
A: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase
B: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0987
Polymers54,6712
Non-polymers4275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-43 kcal/mol
Surface area16670 Å2
MethodPISA
2
C: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase
D: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0987
Polymers54,6712
Non-polymers4275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-43 kcal/mol
Surface area16700 Å2
MethodPISA
3
E: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase
F: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0756
Polymers54,6712
Non-polymers4044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-31 kcal/mol
Surface area17510 Å2
MethodPISA
4
G: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase
H: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0756
Polymers54,6712
Non-polymers4044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-36 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.021, 71.159, 93.183
Angle α, β, γ (deg.)108.390, 102.230, 89.990
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase / Orotidine 5'-phosphate decarboxylase / OMP decarboxylase / OMPDCase / OMPdecase


Mass: 27335.434 Da / Num. of mol.: 8 / Fragment: KlaeA.01229.a.B1 / Mutation: D23E, T133M, A163V, A220V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: pyrF, BXQ27_18035, HV316_11080, KCTC 2190 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0M3H420, orotidine-5'-phosphate decarboxylase
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.94 Å3/Da / Density % sol: 36.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus B4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, 30 mM NaF, 30 mM NaBr and 30 mM NaI, KlaeA.01229.a.B1 at 15 mg/mL with 2.5 GDP added. No electron ...Details: Morpheus B4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, 30 mM NaF, 30 mM NaBr and 30 mM NaI, KlaeA.01229.a.B1 at 15 mg/mL with 2.5 GDP added. No electron density for GDP was observed, Tray: plate 12527 well B4 drop 3, Puck: PSL0811, Cryo: DIRECT

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONNSLS-II 19-ID10.97949
SEALED TUBEBRUKER D8 QUEST21.54184
Detector
TypeIDDetectorDateDetails
DECTRIS EIGER2 XE 9M1PIXELApr 8, 2022
Bruker PHOTON III2PIXELMar 29, 2022Helios Multilayer
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal Si 111SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979491
21.541841
ReflectionResolution: 2→49.41 Å / Num. obs: 108150 / % possible obs: 97.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 33.37 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
2-2.033.70.60753710.758196.9
10.95-49.413.70.0286450.999196.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.8data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2→49.41 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.18 / Phase error: 26.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 5279 4.88 %
Rwork0.1875 102859 -
obs0.1903 108138 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.23 Å2 / Biso mean: 41.4744 Å2 / Biso min: 16.78 Å2
Refinement stepCycle: final / Resolution: 2→49.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12802 0 18 390 13210
Biso mean--58.82 39.58 -
Num. residues----1753
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.020.31381690.25783493366297
2.02-2.050.3561840.2663312349697
2.05-2.070.31091690.25243440360997
2.07-2.10.29351650.24973418358397
2.1-2.130.32421660.25023385355197
2.13-2.150.31111620.24393501366397
2.15-2.190.30941790.24223294347397
2.19-2.220.28881630.23133513367697
2.22-2.250.30771760.22953370354697
2.25-2.290.32341440.22863461360597
2.29-2.330.25382040.22373356356097
2.33-2.370.29081770.21933465364298
2.37-2.420.29461800.20763379355997
2.42-2.470.26051830.2073517370098
2.47-2.520.251750.2043376355198
2.52-2.580.30141470.21513470361798
2.58-2.640.28161820.21363452363498
2.64-2.710.29151920.22063398359098
2.71-2.790.2921920.20623433362598
2.79-2.880.26981740.20083468364298
2.88-2.990.24651920.19893433362598
2.99-3.110.25771750.20333460363598
3.11-3.250.25272060.20093373357998
3.25-3.420.26111980.19033448364698
3.42-3.630.23151640.17483439360398
3.63-3.910.22031390.15853423356297
3.91-4.310.20261660.14913424359096
4.31-4.930.15481660.13233428359498
4.93-6.210.23112370.16843440367799
6.21-49.410.20091530.1653490364399

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