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- PDB-2f8m: Ribose 5-phosphate isomerase from Plasmodium falciparum -

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Basic information

Entry
Database: PDB / ID: 2f8m
TitleRibose 5-phosphate isomerase from Plasmodium falciparum
Componentsribose 5-phosphate isomerase
KeywordsISOMERASE / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / STRUCTURAL GENOMICS OF PATHOGENIC PROTOZOA CONSORTIUM / SGPP
Function / homology
Function and homology information


ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch
Similarity search - Function
Ribose 5-phosphate isomerase, type A / Ribose 5-phosphate isomerase A (phosphoriboisomerase A) / Rossmann fold - #1360 / ACT domain / NagB/RpiA transferase-like / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Ribose-5-phosphate isomerase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.087 Å
AuthorsHolmes, M.A. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Structure of ribose 5-phosphate isomerase from Plasmodium falciparum.
Authors: Holmes, M.A. / Buckner, F.S. / Van Voorhis, W.C. / Verlinde, C.L. / Mehlin, C. / Boni, E. / DeTitta, G. / Luft, J. / Lauricella, A. / Anderson, L. / Kalyuzhniy, O. / Zucker, F. / Schoenfeld, ...Authors: Holmes, M.A. / Buckner, F.S. / Van Voorhis, W.C. / Verlinde, C.L. / Mehlin, C. / Boni, E. / DeTitta, G. / Luft, J. / Lauricella, A. / Anderson, L. / Kalyuzhniy, O. / Zucker, F. / Schoenfeld, L.W. / Earnest, T.N. / Hol, W.G. / Merritt, E.A.
History
DepositionDec 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.description / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: ribose 5-phosphate isomerase
B: ribose 5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6574
Polymers54,4672
Non-polymers1902
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-32 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.689, 136.230, 45.011
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is the dimer in the asymmetric unit.

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Components

#1: Protein ribose 5-phosphate isomerase


Mass: 27233.689 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PFE0730c / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: Q8I3W2, ribose-5-phosphate isomerase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.4 ul protein 8 mg/ml, 0.4 ul crystallization buffer 200mM NaCl, 0.6 mM KAu(CN)2, 20% PEG 3000,100 mM HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.03492 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03492 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 32530 / % possible obs: 92.7 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.073 / Χ2: 1.896 / Net I/σ(I): 25.818
Reflection shellHighest resolution: 2.08 Å / % possible obs: 96.6 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 3.916 / Num. measured obs: 3332 / Χ2: 0.989 / % possible all: 96.6

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Phasing

Phasing MRRfactor: 0.598 / Cor.coef. Fo:Fc: 0.169
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
EPMR2.5phasing
PDB_EXTRACT1.7data extraction
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.2.0005 24/04/2001refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UJ5

1uj5


Resolution: 2.087→50 Å / SU B: 8.291 / SU ML: 0.206 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.213
RfactorNum. reflectionSelection details
Rfree0.2716 1571 random
Rwork0.2085 --
obs-31605 -
Displacement parametersBiso mean: 25.8 Å2
Refinement stepCycle: LAST / Resolution: 2.087→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3595 0 10 226 3831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223646
X-RAY DIFFRACTIONr_bond_other_d0.0010.023472
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.9874935
X-RAY DIFFRACTIONr_angle_other_deg0.7238064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6835470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.76325.113133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0215678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5651514
X-RAY DIFFRACTIONr_chiral_restr0.0530.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023960
X-RAY DIFFRACTIONr_gen_planes_other00.02662
X-RAY DIFFRACTIONr_nbd_refined0.2080.3742
X-RAY DIFFRACTIONr_nbd_other0.1990.33522
X-RAY DIFFRACTIONr_nbtor_refined0.1830.51771
X-RAY DIFFRACTIONr_nbtor_other0.0950.52124
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.5359
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0310.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.312
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2210.336
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.56
X-RAY DIFFRACTIONr_mcbond_it1.34922377
X-RAY DIFFRACTIONr_mcbond_other0.272979
X-RAY DIFFRACTIONr_mcangle_it2.22733773
X-RAY DIFFRACTIONr_mcangle_other1.02733140
X-RAY DIFFRACTIONr_scbond_it3.07841394
X-RAY DIFFRACTIONr_scbond_other0.91842770
X-RAY DIFFRACTIONr_scangle_it4.63861162
X-RAY DIFFRACTIONr_scangle_other1.91264924
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.087-2.1410.3211140.282228256691.27
2.141-2.1990.3031200.272254245196.858
2.199-2.2630.654340.483713243130.728
2.263-2.3320.284740.2821365234061.496
2.332-2.4090.3121270.2482129230198.044
2.409-2.4930.2881130.2312080222198.739
2.493-2.5870.3131080.2351991211799.15
2.587-2.6920.284910.2261975207599.566
2.692-2.8120.269960.2181912201299.801
2.812-2.9480.263840.2151789187599.893
2.948-3.1070.249880.2051722181199.945
3.107-3.2950.253860.1971627171699.825
3.295-3.5210.233690.18515581627100
3.521-3.8020.296680.2251139152579.148
3.802-4.1620.25700.171113140284.379
4.162-4.650.193640.1341215128199.844
4.65-5.3610.209540.15310901144100
5.361-6.5470.322510.19494099299.899
6.547-9.1810.194400.17174478599.873
9.181-500.302200.21845048297.51

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