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

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Basic information

Entry
Database: PDB / ID: 6dsq
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
orotidine-5'-phosphate decarboxylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 6DSQ REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 2ZA2 DETERMINED BY AUTHOR: ...THIS ENTRY 6DSQ REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 2ZA2 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


Theoretical massNumber of molelcules
Total (without water)75,7322
Polymers75,7322
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-28 kcal/mol
Surface area23150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.812, 201.812, 44.026
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 through 45 or (resid 46...
21(chain B and ((resid 1 and (name N or 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
11METMETLYSLYS(chain A and (resid 1 through 45 or (resid 46...AA1 - 451 - 45
12LYSLYSLYSLYS(chain A and (resid 1 through 45 or (resid 46...AA4646
13METMETASNASN(chain A and (resid 1 through 45 or (resid 46...AA1 - 3201 - 320
14METMETASNASN(chain A and (resid 1 through 45 or (resid 46...AA1 - 3201 - 320
15METMETASNASN(chain A and (resid 1 through 45 or (resid 46...AA1 - 3201 - 320
16METMETASNASN(chain A and (resid 1 through 45 or (resid 46...AA1 - 3201 - 320
21METMETMETMET(chain B and ((resid 1 and (name N or name...BB11
22METMETASNASN(chain B and ((resid 1 and (name N or name...BB1 - 3201 - 320
23METMETASNASN(chain B and ((resid 1 and (name N or name...BB1 - 3201 - 320
24METMETASNASN(chain B and ((resid 1 and (name N or name...BB1 - 3201 - 320
25METMETASNASN(chain B and ((resid 1 and (name N or name...BB1 - 3201 - 320

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 23% PEG 3000, pH 9.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.977 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 18313 / % possible obs: 99.6 % / Redundancy: 3.2 % / Net I/σ(I): 4

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N3M

3n3m


Resolution: 2.7→39.318 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 27.6
RfactorNum. reflection% reflection
Rfree0.2509 1823 9.96 %
Rwork0.1949 --
obs0.2004 18309 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.68 Å2 / Biso mean: 52.5285 Å2 / Biso min: 16.44 Å2
Refinement stepCycle: final / Resolution: 2.7→39.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4979 0 0 33 5012
Biso mean---43.29 -
Num. residues----618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085085
X-RAY DIFFRACTIONf_angle_d0.9716874
X-RAY DIFFRACTIONf_chiral_restr0.055750
X-RAY DIFFRACTIONf_plane_restr0.007883
X-RAY DIFFRACTIONf_dihedral_angle_d4.4043048
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2842X-RAY DIFFRACTION10.752TORSIONAL
12B2842X-RAY DIFFRACTION10.752TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.7730.35631440.29113031447100
2.773-2.85460.3671400.261112601400100
2.8546-2.94670.32491410.241312841425100
2.9467-3.0520.28981390.231412531392100
3.052-3.17410.30631440.222612911435100
3.1741-3.31850.30091380.225912461384100
3.3185-3.49340.27481360.216512671403100
3.4934-3.71210.28821410.20961266140799
3.7121-3.99850.22081430.180912861429100
3.9985-4.40040.24991400.16112601400100
4.4004-5.0360.18161420.15611255139799
5.036-6.34050.23141360.19191264140099
6.3405-39.32210.20091390.16951251139098

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