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

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Basic information

Entry
Database: PDB / ID: 2qaf
TitleCrystal structure of Plasmodium falciparum orotidine 5'-phosphate decarboxylase covalently modified by 6-iodo-UMP
ComponentsOrotidine 5' monophosphate decarboxylase
KeywordsLYASE / Plasmodium falciparum / orotidine 5'-phosphate decarboxylase / covalently / 6-iodo-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
URIDINE-5'-MONOPHOSPHATE / orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Aug 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 600 HETEROGEN The authors state that there is a covalent bond formed between carbon-6 of the uridine ... HETEROGEN The authors state that there is a covalent bond formed between carbon-6 of the uridine ring of UMP and the NZ-nitrogen of Lys138

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Orotidine 5' monophosphate decarboxylase
B: Orotidine 5' monophosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5435
Polymers79,7992
Non-polymers7443
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-48.8 kcal/mol
Surface area24410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.920, 83.849, 89.869
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-3046-

HOH

21A-3073-

HOH

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Components

#1: Protein Orotidine 5' 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: ompdc / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL(DE23)
References: UniProt: Q8T6J6, UniProt: Q8IJH3*PLUS, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.91 Å3/Da / Density % sol: 35.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 30% PEG 1000, 100mM Ammonium phosphate, pH 7.4, 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: 1.95→50 Å / Num. all: 43303 / Num. obs: 41322 / % possible obs: 95.43 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 9.1
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2199 / Rsym value: 0.492 / % possible all: 98

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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: 1.95→28.3 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.455 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.194 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 2191 5.1 %RANDOM
Rwork0.17183 ---
obs0.17453 41065 95.44 %-
all-43027 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.806 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.95→28.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5354 0 47 250 5651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225589
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.9687549
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1985661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.40325.764288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8151018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1521513
X-RAY DIFFRACTIONr_chiral_restr0.120.2804
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024241
X-RAY DIFFRACTIONr_nbd_refined0.2320.22697
X-RAY DIFFRACTIONr_nbtor_refined0.3150.23941
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2313
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.211
X-RAY DIFFRACTIONr_mcbond_it1.1521.53386
X-RAY DIFFRACTIONr_mcangle_it1.7325337
X-RAY DIFFRACTIONr_scbond_it2.88532536
X-RAY DIFFRACTIONr_scangle_it4.1884.52212
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 152 -
Rwork0.187 2955 -
obs-3107 95.34 %

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