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- PDB-3n34: Crystal structure of Plasmodium falciparum orotidine 5'-monophosp... -

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Basic information

Entry
Database: PDB / ID: 3n34
TitleCrystal structure of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase complexed with 5-fluoro-6-amino-UMP, produced from 5-fluoro-6-azido-UMP
ComponentsOrotidine 5'-phosphate decarboxylase
KeywordsLYASE / P. falciparum / orotidine 5'-monophosphate decarboxylase / 5-fluoro-6-amino-UMP / 5-fluoro-6-azido-UMP
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, type 2 / 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, type 2 / 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
6-amino-5-fluorouridine 5'-(dihydrogen phosphate) / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / orotidine-5'-phosphate decarboxylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLiu, Y. / Kotra, L.P. / Pai, E.F.
CitationJournal: To be Published
Title: Crystal structure of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase complexed with 5-fluoro-6-amino-UMP, produced from 5-fluoro-6-azido-UMP
Authors: Liu, Y. / Kotra, L.P. / Pai, E.F.
History
DepositionMay 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9278
Polymers79,7992
Non-polymers1,1286
Water10,431579
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-25 kcal/mol
Surface area24260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.339, 83.085, 89.857
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Orotidine 5'-phosphate decarboxylase


Mass: 39899.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: gi|9310996, PF10_0225 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8IJH3, orotidine-5'-phosphate decarboxylase

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Non-polymers , 6 types, 585 molecules

#2: Chemical ChemComp-FNU / 6-amino-5-fluorouridine 5'-(dihydrogen phosphate)


Type: DNA linking / Mass: 357.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13FN3O9P
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H2O

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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: 1.88 Å3/Da / Density % sol: 34.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: PEG1000, ammonium phosphate, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 87273 / Num. obs: 83977 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 10.5
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4338 / Rsym value: 0.441 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q8L

2q8l


Resolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.312 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18185 4373 5 %RANDOM
Rwork0.15565 ---
obs0.15699 82847 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.356 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2---0.11 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5337 0 72 579 5988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226020
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9638197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9875750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.55125.871310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.004151100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5681513
X-RAY DIFFRACTIONr_chiral_restr0.1080.2855
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214710
X-RAY DIFFRACTIONr_mcbond_it0.8331.53549
X-RAY DIFFRACTIONr_mcangle_it1.50825826
X-RAY DIFFRACTIONr_scbond_it2.43732471
X-RAY DIFFRACTIONr_scangle_it3.9674.52371
LS refinement shellResolution: 1.551→1.592 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 315 -
Rwork0.196 5927 -
obs-6242 97.36 %

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