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- PDB-2ffc: Crystal Structure of Plasmodium Vivax Orotidine-Monophosphate-Dec... -

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Basic information

Entry
Database: PDB / ID: 2ffc
TitleCrystal Structure of Plasmodium Vivax Orotidine-Monophosphate-Decarboxyl UMP Bound
Componentsorotidine 5-monophosphate decarboxylase
KeywordsLYASE / DECARBOXYLASE / PV-PF10_0225 / SGC / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / URIDINE-5'-MONOPHOSPHATE
Function and homology information
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDong, A. / Wasney, G. / Vedadi, M. / Lew, J. / Koeieradzki, I. / Zhao, Y. / Edwards, A.M. / Melone, M. / Arrowsmith, C.H. / Weigelt, J. ...Dong, A. / Wasney, G. / Vedadi, M. / Lew, J. / Koeieradzki, I. / Zhao, Y. / Edwards, A.M. / Melone, M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Amani, M. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2007
Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R.
History
DepositionDec 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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
Remark 999Sequence No suitable database references were found at time of processing

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: orotidine 5-monophosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5162
Polymers40,1921
Non-polymers3241
Water5,729318
1
A: orotidine 5-monophosphate decarboxylase
hetero molecules

A: orotidine 5-monophosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0324
Polymers80,3832
Non-polymers6482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6250 Å2
ΔGint-40 kcal/mol
Surface area23060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.817, 69.588, 59.338
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-5505-

HOH

21A-5506-

HOH

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Components

#1: Protein orotidine 5-monophosphate decarboxylase


Mass: 40191.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Plasmid: P28-LIC-THROMBIN DERIVED FROM PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon plus Ril / References: EC: 4.1.3.23
#2: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.1 Å3/Da / Density % sol: 41.45 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 8.5
Details: 30.0% PEG 4K, 0.2M NaOAc, 0.1M Tris HCl, VAPOR DIFFUSION, pH 8.5, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: SBC-3 / Detector: CCD / Date: Nov 5, 2005 / Details: Si 111
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 37109 / Num. obs: 37109 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 10.2
Reflection shellResolution: 1.7→1.72 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1473 / Rsym value: 0.612 / % possible all: 80.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data scaling
PHASERV. 1.3.1phasing
Coot0.0.33model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AQW

2aqw


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.442 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.112 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23444 944 2.5 %RANDOM
Rwork0.18703 ---
all0.18825 36127 --
obs0.18825 36127 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.437 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20 Å2
2--0.22 Å20 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 21 318 2909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222652
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.9723570
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7475317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82925132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23715487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7141511
X-RAY DIFFRACTIONr_chiral_restr0.120.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021996
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.21362
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21864
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1791.51636
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71922546
X-RAY DIFFRACTIONr_scbond_it2.74631157
X-RAY DIFFRACTIONr_scangle_it4.1994.51024
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 60 -
Rwork0.279 2239 -
obs--83.81 %

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