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- PDB-1m7o: Plasmodium Falciparum Triosephosphate isomerase (PfTIM) compled t... -

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Basic information

Entry
Database: PDB / ID: 1m7o
TitlePlasmodium Falciparum Triosephosphate isomerase (PfTIM) compled to substrate analog 3-phosphoglycerate (3PG)
ComponentsTriosephosphate Isomerase
KeywordsISOMERASE / TIM barrels / beta-alpha barrels / enzyme-inhibitor complex
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / identical protein binding / cytosol
Similarity search - Function
Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
3-PHOSPHOGLYCERIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsParthasarathy, S. / Balaram, H. / Balaram, P. / Murthy, M.R.N.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structures of Plasmodium falciparum triosephosphate isomerase complexed to substrate analogues: observation of the catalytic loop in the open conformation in the ligand-bound state.
Authors: Parthasarathy, S. / Balaram, H. / Balaram, P. / Murthy, M.R.
#1: Journal: Structure / Year: 1997
Title: Triosephosphate Isomerase From Plasmodium Falciparum: Crystal Structure Proveides Insights into Antimalarial Drug Design.
Authors: Velankar, S.S. / Ray, S.S. / Gokle, R.S. / Suma, S. / Balaram, H. / Balaram, P. / Murthy, M.R.N.
History
DepositionJul 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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

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Assembly

Deposited unit
A: Triosephosphate Isomerase
B: Triosephosphate Isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3684
Polymers55,9952
Non-polymers3722
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-31 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.260, 51.345, 90.360
Angle α, β, γ (deg.)90.00, 91.38, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein Triosephosphate Isomerase / E.C.5.3.1.1 / TIM / triose-phosphate isomerase / triose phosphate isomerase


Mass: 27997.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: TPI / Plasmid: ptrc 99A vector, called pARC / Production host: Escherichia coli (E. coli) / Strain (production host): AA200 / References: UniProt: Q07412, triose-phosphate isomerase
#2: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.26 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 12% to 20% PEG 1450 in 100mm Sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP at 295K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18-24 %PEG14501reservoir
2100 mMsodium acetate1reservoirpH7.5
310 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 9, 1999 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 19146 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 18.3 Å2 / Rsym value: 0.116 / Net I/σ(I): 10.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 1868 / Rsym value: 0.399 / % possible all: 95.3
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. measured all: 73117 / Rmerge(I) obs: 0.116
Reflection shell
*PLUS
% possible obs: 95.3 % / Rmerge(I) obs: 0.399

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Unbound PfTIM; PDB CODE 1YDV

1ydv


Resolution: 2.4→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 165654.6 / Data cutoff high rms absF: 165654.6 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.1 / σ(I): 165654.6 / Stereochemistry target values: Engh & Huber
Details: Maximum Likelihood in Amplitute (MLF) is employed. Anisotropic B-value scaling, Bulk solvent correction and 2-fold NCS restraint were used throughout the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1811 9.8 %RANDOM
Rwork0.183 ---
all-19146 --
obs-18389 93.3 %-
Solvent computationBsol: 31.1851 Å2 / ksol: 0.316133 e/Å3
Displacement parametersBiso mean: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.95 Å21.42 Å23.53 Å2
2--0 Å20.9 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3914 0 22 130 4066
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.442.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 290 10.3 %
Rwork0.234 2532 -
obs-2532 86.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION33pg.par3pg.top
Refinement
*PLUS
Highest resolution: 2.4 Å / Rfactor Rfree: 0.226 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.782
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1
LS refinement shell
*PLUS
Rfactor Rfree: 0.29 / Rfactor Rwork: 0.234

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