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- PDB-2fds: Crystal Structure of Plasmodium Berghei Orotidine 5'-monophosphat... -

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Basic information

Entry
Database: PDB / ID: 2fds
TitleCrystal Structure of Plasmodium Berghei Orotidine 5'-monophosphate Decarboxylase (ortholog of Plasmodium falciparum PF10_0225)
Componentsorotidine-monophosphate-decarboxylase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / TIM barrel / Structural Genomics Consortium / SGC
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / IODIDE ION / :
Function and homology information
Biological speciesPlasmodium berghei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsQiu, W. / Dong, A. / Wasney, G. / Vedadi, M. / Lew, J. / Kozieradski, I. / Alam, Z. / Melone, M. / Weigelt, J. / Sundstrom, M. ...Qiu, W. / Dong, A. / Wasney, G. / Vedadi, M. / Lew, J. / Kozieradski, I. / Alam, Z. / Melone, M. / Weigelt, J. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Hui, R. / Gao, M. / Bochkarev, A. / Artz, J.D. / 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 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)82,2994
Polymers82,0452
Non-polymers2542
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-28 kcal/mol
Surface area24870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.202, 108.623, 69.890
Angle α, β, γ (deg.)90.00, 97.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein orotidine-monophosphate-decarboxylase


Mass: 41022.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium berghei (eukaryote) / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4Z4C3
#2: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.03 Å3/Da / Density % sol: 39.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 16% Peg3350, 140mM diammonium hydrogen citrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 31, 2005
Radiation
IDProtocolScattering typeWavelength-ID
1SINGLE WAVELENGTHx-ray1
2x-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 65456 / % possible obs: 94.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.047 / Χ2: 1.849
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.72-1.781.90.38246371.03767
1.78-1.852.30.28663011.15491
1.85-1.943.10.22868231.3798.8
1.94-2.043.10.15468181.42899.3
2.04-2.173.10.10568861.59199.6
2.17-2.332.90.08166781.71495.9
2.33-2.573.20.06268631.82699.4
2.57-2.943.20.04969132.02899.6
2.94-3.713.20.03665652.29194.2
3.71-503.20.03269723.04399.3

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3 Å35.09 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 2AQW

2aqw


Resolution: 1.72→29.22 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.398 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3308 5.1 %RANDOM
Rwork0.186 ---
all0.188 ---
obs-65422 94.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.168 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.72→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5438 0 2 328 5768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225537
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9517475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7155671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.67425.864295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.629151050
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9321516
X-RAY DIFFRACTIONr_chiral_restr0.1050.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024246
X-RAY DIFFRACTIONr_nbd_refined0.2140.22879
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23980
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2382
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.210
X-RAY DIFFRACTIONr_mcbond_it1.27623325
X-RAY DIFFRACTIONr_mcangle_it2.03435371
X-RAY DIFFRACTIONr_scbond_it1.37422426
X-RAY DIFFRACTIONr_scangle_it2.02832104
LS refinement shellResolution: 1.719→1.764 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.558 148 -
Rwork0.409 2978 -
obs-3126 61.01 %

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