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- PDB-2q8l: Crystal structure of orotidine 5'-phosphate decarboxylase from Pl... -

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Basic information

Entry
Database: PDB / ID: 2q8l
TitleCrystal structure of orotidine 5'-phosphate decarboxylase from Plasmodium falciparum
ComponentsOrotidine-monophosphate-decarboxylase
KeywordsLYASE / Plasmodium falciparum / orotidine-5'-monophosphate decarboxylase / Structural Genomics / Structural Genomics Consortium / SGC
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
PHOSPHATE ION / orotidine-5'-phosphate decarboxylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiu, Y. / Lau, W. / Lew, J. / Amani, M. / Hui, R. / Pai, E.F. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of orotidine 5'-phosphate decarboxylase from Plasmodium falciparum.
Authors: Liu, Y. / Lau, W. / Lew, J. / Amani, M. / Hui, R. / Pai, E.F.
History
DepositionJun 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9612
Polymers37,8661
Non-polymers951
Water2,558142
1
A: Orotidine-monophosphate-decarboxylase
hetero molecules

A: Orotidine-monophosphate-decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9224
Polymers75,7322
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Unit cell
Length a, b, c (Å)68.563, 70.909, 70.201
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe second part of the biological assembly is generated by the two fold axis: -X,-Y, Z.

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Components

#1: Protein Orotidine-monophosphate-decarboxylase / Orotidine 5'-phosphate decarboxylase


Mass: 37866.246 Da / Num. of mol.: 1
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(DE3) / References: UniProt: Q8IJH3
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 10000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978565 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 29, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.1→24.95 Å / Num. all: 19423 / Num. obs: 19423 / % possible obs: 97.15 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 11.8
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 7.39 / Num. unique all: 1015 / Rsym value: 0.267 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2F84

2f84


Resolution: 2.1→24.95 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.43 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.265 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Program CNS 1.0 was also used in the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.24929 597 3 %RANDOM
Rwork0.21643 ---
all0.21746 19423 --
obs0.21746 19423 97.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.622 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å20 Å20 Å2
2---0.11 Å20 Å2
3---1.88 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 5 142 2740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222660
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9583585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3155313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.85325.652138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.19215492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.714156
X-RAY DIFFRACTIONr_chiral_restr0.1170.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022017
X-RAY DIFFRACTIONr_nbd_refined0.2120.21326
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21863
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2179
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.29
X-RAY DIFFRACTIONr_mcbond_it1.2581.51612
X-RAY DIFFRACTIONr_mcangle_it1.61822547
X-RAY DIFFRACTIONr_scbond_it2.72931185
X-RAY DIFFRACTIONr_scangle_it3.4674.51038
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 46 -
Rwork0.258 1379 -
obs-1425 94.62 %

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