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- PDB-8ek7: Crystal structure of Hepes and Mg bound 2,3-diketo-5-methylthiope... -

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Basic information

Entry
Database: PDB / ID: 8ek7
TitleCrystal structure of Hepes and Mg bound 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from Klebsiella aerogenes
ComponentsOrotidine 5'-phosphate decarboxylase
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-type TIM barrel
Similarity search - Domain/homology
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 / 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)HHSN272201700059C United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Hepes and Mg bound 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from Klebsiella aerogenes
Authors: Lovell, S. / Liu, L. / Seibold, S. / Battaile, K.P.
History
DepositionSep 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 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: Orotidine 5'-phosphate decarboxylase
B: Orotidine 5'-phosphate decarboxylase
C: Orotidine 5'-phosphate decarboxylase
D: Orotidine 5'-phosphate decarboxylase
E: Orotidine 5'-phosphate decarboxylase
F: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,64024
Polymers164,0916
Non-polymers1,54918
Water12,340685
1
A: Orotidine 5'-phosphate decarboxylase
B: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2699
Polymers54,6972
Non-polymers5727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-67 kcal/mol
Surface area17660 Å2
MethodPISA
2
C: Orotidine 5'-phosphate decarboxylase
D: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1267
Polymers54,6972
Non-polymers4295
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-49 kcal/mol
Surface area17750 Å2
MethodPISA
3
E: Orotidine 5'-phosphate decarboxylase
F: Orotidine 5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2448
Polymers54,6972
Non-polymers5486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-61 kcal/mol
Surface area17550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.517, 70.141, 115.985
Angle α, β, γ (deg.)90.000, 93.340, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Orotidine 5'-phosphate decarboxylase / OMP decarboxylase / OMPDCase / OMPdecase


Mass: 27348.453 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: pyrF, BXQ27_18035, HV316_11080 / Plasmid: KlaeA.01229.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0M3H420, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 685 / 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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus A8: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM HEPES/MOPS, pH 7.5, 30 mM MgCl2 and 30 mM CaCl2, KlaeA.01229.a.B1.PW39096 at 15 mg/mL. plate 12527, well A8 drop ...Details: Morpheus A8: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM HEPES/MOPS, pH 7.5, 30 mM MgCl2 and 30 mM CaCl2, KlaeA.01229.a.B1.PW39096 at 15 mg/mL. plate 12527, well A8 drop 3, Puck: PSL0308, 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: 0.97856 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 11, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.65→49.41 Å / Num. obs: 160347 / % possible obs: 99.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 18.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Net I/σ(I): 11.5 / Num. measured all: 581276 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.5 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.65-1.680.5622788779040.882.199.6
9.04-49.410.021353610220.99927.597.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimless0.7.9data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8DOP

8dop


Resolution: 1.65→41.69 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 28.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2303 8019 5.02 %
Rwork0.1835 151838 -
obs0.1858 159857 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.72 Å2 / Biso mean: 27.0597 Å2 / Biso min: 9.17 Å2
Refinement stepCycle: final / Resolution: 1.65→41.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9842 0 95 685 10622
Biso mean--35.42 31.55 -
Num. residues----1311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910098
X-RAY DIFFRACTIONf_angle_d0.99913705
X-RAY DIFFRACTIONf_chiral_restr0.0591628
X-RAY DIFFRACTIONf_plane_restr0.0091769
X-RAY DIFFRACTIONf_dihedral_angle_d13.8533717
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 (%)
1.65-1.670.29812560.237750525308100
1.67-1.690.30012830.242349695252100
1.69-1.710.27092410.232151375378100
1.71-1.730.29772590.217350555314100
1.73-1.750.2772370.207550725309100
1.75-1.780.25662540.198450305284100
1.78-1.80.27752520.208350575309100
1.8-1.830.26982750.195650795354100
1.83-1.860.26432700.19275037530799
1.86-1.890.27892640.189550505314100
1.89-1.920.27012650.18255036530199
1.92-1.960.23332640.17435068533299
1.96-1.990.22382860.17635051533799
1.99-2.030.23532470.166250795326100
2.03-2.080.21232360.16995057529399
2.08-2.130.2252610.1725072533399
2.13-2.180.25982820.179850445326100
2.18-2.240.19772740.168250245298100
2.24-2.310.22742790.167750935372100
2.31-2.380.22072950.162250315326100
2.38-2.460.20122850.153850715356100
2.46-2.560.21623030.160950145317100
2.56-2.680.24783270.172850425369100
2.68-2.820.21522850.1775088537399
2.82-30.21412510.18195051530299
3-3.230.21382420.18375074531699
3.23-3.550.19552510.17775071532299
3.55-4.070.23012670.17225107537499
4.07-5.120.20032580.18195137539599
5.12-41.690.26882700.23535090536096

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