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

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Basic information

Entry
Database: PDB / ID: 8doq
TitleCrystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from Klebsiella aerogenes (P21 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
BENZOIC ACID / Orotidine 5'-phosphate decarboxylase
Similarity search - Component
Biological speciesKlebsiella aerogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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: Liu, L. / Seibold, S. / Battaile, K.P. / Lovell, S.
History
DepositionJul 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 22, 2023Group: Data collection / Category: diffrn / Item: _diffrn.ambient_temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0295
Polymers54,6712
Non-polymers3583
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-37 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.350, 70.500, 66.840
Angle α, β, γ (deg.)90.000, 90.910, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 2 / Fragment: KlaeA.01229.a.B1 / Mutation: D42E, T152M, A182V, A239V
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-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.13 Å3/Da / Density % sol: 42.16 %
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, 30 mM MgCl2 and 30 mM CaCl2, KlaeA.01229.a.B1 at 15 mg/mL, Tray: plate 12527 well A4 drop 1, Puck: ...Details: Morpheus A4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, 30 mM MgCl2 and 30 mM CaCl2, KlaeA.01229.a.B1 at 15 mg/mL, Tray: plate 12527 well A4 drop 1, Puck: PSL0809, Cryo: DIRECT; Electron density consistent with a benzoic acid molecule was observed and modeled. The source of this is unknown and it may have been acquired from the expression host

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 8, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.65→70.5 Å / Num. obs: 55090 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 16.81 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.058 / Rrim(I) all: 0.111 / Net I/σ(I): 6.4 / Num. measured all: 194613 / Scaling rejects: 181
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.6 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.65-1.690.3551453140270.8960.2180.4182.299.6
7.38-70.50.07122976440.9860.0440.08412.898.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8DOP

8dop


Resolution: 1.65→39.4 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2094 2718 4.94 %
Rwork0.1791 52290 -
obs0.1807 55008 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.18 Å2 / Biso mean: 26.6252 Å2 / Biso min: 9.69 Å2
Refinement stepCycle: final / Resolution: 1.65→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 0 25 307 3594
Biso mean--28.09 30.42 -
Num. residues----437
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.680.27981600.24092696285699
1.68-1.710.30691300.217727502880100
1.71-1.750.24161640.201926862850100
1.75-1.790.26271450.20232734287999
1.79-1.830.24811370.209727552892100
1.83-1.870.26531040.20427782882100
1.87-1.920.20461080.198427612869100
1.92-1.980.23181290.18227762905100
1.98-2.040.22051480.182427452893100
2.04-2.120.22631190.1827422861100
2.12-2.20.21731560.184127612917100
2.2-2.30.24361120.172727732885100
2.3-2.420.21561590.177927462905100
2.42-2.570.20031610.174727402901100
2.57-2.770.23251680.178427462914100
2.77-3.050.20721620.181627462908100
3.05-3.490.18451490.172627632912100
3.49-4.40.17121390.156327932932100
4.4-39.40.18871680.17352799296799
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)
11.2414-0.25490.06592.09240.36191.48890.0371-0.1913-0.17340.15130.0312-0.06470.20040.1024-0.07250.1517-0.01110.05260.10260.01920.166719.6398-13.41669.6645
23.02010.00310.50641.2818-0.28981.01590.0997-0.12220.14270.0326-0.01360.051-0.1639-0.1012-0.07040.16140.00150.09620.09630.00880.1769.21422.7356.1023
30.6612-0.6996-0.37924.10670.4840.50320.17940.1313-0.0142-0.4877-0.15680.1682-0.1611-0.1316-0.02450.21460.0270.05190.10560.00880.165811.292-10.2509-5.1912
41.2806-0.24180.00861.67980.47223.3679-0.0797-0.1755-0.00030.5260.1821-0.16470.19870.4227-0.0870.32360.04460.02670.2058-0.00770.184515.3049-7.54529.5606
50.8924-0.45110.47651.61960.61112.17580.1089-0.09040.16490.0691-0.01330.0585-0.1872-0.3223-0.08250.24940.03310.15480.20640.00520.2706-0.21360.114520.5664
62.75320.04230.92611.2551.10713.3793-0.0926-0.24720.23920.41430.050.0857-0.1834-0.14940.03810.43180.01790.10250.1861-0.00740.21486.26335.651836.0239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 111)A20 - 111
2X-RAY DIFFRACTION2chain 'A' and (resid 112 through 168 )A112 - 168
3X-RAY DIFFRACTION3chain 'A' and (resid 169 through 249 )A169 - 249
4X-RAY DIFFRACTION4chain 'B' and (resid 20 through 111 )B20 - 111
5X-RAY DIFFRACTION5chain 'B' and (resid 112 through 168 )B112 - 168
6X-RAY DIFFRACTION6chain 'B' and (resid 169 through 249 )B169 - 249

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