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- PDB-2q8z: Crystal structure of Plasmodium falciparum orotidine 5'-phosphate... -

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Basic information

Entry
Database: PDB / ID: 2q8z
TitleCrystal structure of Plasmodium falciparum orotidine 5'-phosphate decarboxylase complexed with 6-amino-UMP
ComponentsOrotidine-monophosphate-decarboxylase
KeywordsLYASE / Plasmodium falciparum / orotidine 5'-phosphate decarboxylase / 6-amino-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
Chem-7PE / 6-AMINOURIDINE 5'-MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / orotidine-5'-phosphate decarboxylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLiu, Y. / Lau, W. / Bello, A.M. / Kotra, L.P. / Hui, R. / Pai, E.F.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Structure-Activity Relationships of C6-Uridine Derivatives Targeting Plasmodia Orotidine Monophosphate Decarboxylase.
Authors: Bello, A.M. / Poduch, E. / Liu, Y. / Wei, L. / Crandall, I. / Wang, X. / Dyanand, C. / Kain, K.C. / Pai, E.F. / Kotra, L.P.
History
DepositionJun 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 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

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Assembly

Deposited unit
A: Orotidine-monophosphate-decarboxylase
B: Orotidine-monophosphate-decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1929
Polymers79,7992
Non-polymers1,3937
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-70 kcal/mol
Surface area24490 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.497, 83.885, 89.608
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-747-

HOH

21A-775-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Orotidine-monophosphate-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: PF10_0225 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL(DE23) / References: UniProt: Q8IJH3

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Non-polymers , 5 types, 264 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NUP / 6-AMINOURIDINE 5'-MONOPHOSPHATE


Mass: 339.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O9P
#4: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT


Mass: 310.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 1.96 Å3/Da / Density % sol: 37.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG 1000, 100mM Ammonium phosphate, pH 7.0, 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 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 51328 / Num. obs: 51328 / % possible obs: 94.41 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 10.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2826 / Rsym value: 0.435 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Q8L

2q8l


Resolution: 1.8→24.57 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.465 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.141 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21171 2752 5.1 %RANDOM
Rwork0.16693 ---
all0.16916 51328 --
obs0.16916 51328 94.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.266 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--0.8 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5354 0 72 257 5683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225676
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9697678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2695679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.90325.694288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.657151038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0861513
X-RAY DIFFRACTIONr_chiral_restr0.110.2814
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024323
X-RAY DIFFRACTIONr_nbd_refined0.2090.22809
X-RAY DIFFRACTIONr_nbtor_refined0.3170.24041
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2309
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2920.217
X-RAY DIFFRACTIONr_mcbond_it1.0851.53430
X-RAY DIFFRACTIONr_mcangle_it1.67325430
X-RAY DIFFRACTIONr_scbond_it2.73632562
X-RAY DIFFRACTIONr_scangle_it4.0584.52248
LS refinement shellResolution: 1.8→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 216 -
Rwork0.191 3727 -
obs-3943 94.24 %

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