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- PDB-6dsr: Re-refinement of P. falciparum orotidine 5'-monophosphate decarbo... -

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Basic information

Entry
Database: PDB / ID: 6dsr
TitleRe-refinement of P. falciparum orotidine 5'-monophosphate decarboxylase
ComponentsOrotidine 5'-monophosphate decarboxylase
KeywordsLYASE / Complex / P falciparum
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
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.597 Å
AuthorsBrandt, G.S. / Novak, W.R.P.
CitationJournal: J. Biochem. / Year: 2008
Title: Structural basis for the decarboxylation of orotidine 5'-monophosphate (OMP) by Plasmodium falciparum OMP decarboxylase.
Authors: Tokuoka, K. / Kusakari, Y. / Krungkrai, S.R. / Matsumura, H. / Kai, Y. / Krungkrai, J. / Horii, T. / Inoue, T.
History
DepositionJun 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 0THIS ENTRY 6DSR REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 2ZA1 DETERMINED BY AUTHOR: ...THIS ENTRY 6DSR REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 2ZA1 DETERMINED BY AUTHOR: Tokuoka, K., Inoue, T.

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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)76,3814
Polymers75,7322
Non-polymers6482
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-35 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.879, 201.879, 44.191
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 1 and (name N or name...
21(chain B and (resseq 1:38 or (resid 39 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETMETMET(chain A and ((resid 1 and (name N or name...AA11
12METMETASNASN(chain A and ((resid 1 and (name N or name...AA1 - 3201 - 320
13METMETASNASN(chain A and ((resid 1 and (name N or name...AA1 - 3201 - 320
14METMETASNASN(chain A and ((resid 1 and (name N or name...AA1 - 3201 - 320
15METMETASNASN(chain A and ((resid 1 and (name N or name...AA1 - 3201 - 320
21METMETGLUGLU(chain B and (resseq 1:38 or (resid 39 and (name...BB1 - 381 - 38
22ASNASNASNASN(chain B and (resseq 1:38 or (resid 39 and (name...BB3939
23METMETLEULEU(chain B and (resseq 1:38 or (resid 39 and (name...BB1 - 3171 - 317

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Components

#1: Protein Orotidine 5'-monophosphate decarboxylase


Mass: 37866.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: ompdc / Production host: Escherichia coli (E. coli)
References: UniProt: Q8T6J6, 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 23% PEG 3000, pH 9.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.597→36.734 Å / Num. obs: 20677 / % possible obs: 98.8 % / Redundancy: 4 % / Net I/σ(I): 4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N3M

3n3m


Resolution: 2.597→36.734 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 24.83
RfactorNum. reflection% reflection
Rfree0.2244 1049 5.14 %
Rwork0.1825 --
obs0.1846 20423 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.78 Å2 / Biso mean: 53.3047 Å2 / Biso min: 25.65 Å2
Refinement stepCycle: final / Resolution: 2.597→36.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4998 0 42 54 5094
Biso mean--52.33 48.91 -
Num. residues----625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045149
X-RAY DIFFRACTIONf_angle_d0.7156973
X-RAY DIFFRACTIONf_chiral_restr0.05762
X-RAY DIFFRACTIONf_plane_restr0.005894
X-RAY DIFFRACTIONf_dihedral_angle_d12.5083057
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2734X-RAY DIFFRACTION7.734TORSIONAL
12B2734X-RAY DIFFRACTION7.734TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5968-2.73370.32461510.24262752290398
2.7337-2.90490.30121540.23012736289098
2.9049-3.12910.28011610.22532746290798
3.1291-3.44370.29421330.20872805293898
3.4437-3.94160.22391620.17627712933100
3.9416-4.9640.18341500.154627992949100
4.964-36.73750.17811380.1642765290398

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