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- PDB-5bnk: Crystal structure of T75C mutant of Triosephosphate isomerase fro... -

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Basic information

Entry
Database: PDB / ID: 5bnk
TitleCrystal structure of T75C mutant of Triosephosphate isomerase from Plasmodium falciparum
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM Barrel
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
Triosephosphate isomerase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBandyopadhyay, D. / Murthy, M.R.N. / Balaram, H. / Balaram, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology India
CitationJournal: Febs J. / Year: 2015
Title: Probing the role of highly conserved residues in triosephosphate isomerase - analysis of site specific mutants at positions 64 and 75 in the Plasmodial enzyme
Authors: Bandyopadhyay, D. / Murthy, M.R. / Balaram, H. / Balaram, P.
History
DepositionMay 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3Nov 8, 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 / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)56,1706
Polymers56,0002
Non-polymers1704
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-39 kcal/mol
Surface area18550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.360, 76.880, 74.480
Angle α, β, γ (deg.)90.000, 97.790, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Triosephosphate isomerase / TIM / Triose-phosphate isomerase


Mass: 27999.777 Da / Num. of mol.: 2 / Mutation: T75C, A163V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: TPI / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): AA200 / References: UniProt: Q07412, triose-phosphate isomerase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.01 Å3/Da / Density % sol: 38.75 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% PEG 1450, 100mM HEPES, 10 mM calcium chloride, 0.5 mM EDTA, 0.5 mM DTT, 0.5 mM sodium azide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2014
RadiationMonochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.8→73.792 Å / Num. all: 40771 / Num. obs: 40771 / % possible obs: 100 % / Redundancy: 4.1 % / Rpim(I) all: 0.032 / Rrim(I) all: 0.066 / Rsym value: 0.058 / Net I/av σ(I): 7.687 / Net I/σ(I): 12.6 / Num. measured all: 167317
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.94.10.5931.22401459020.3360.5932.2100
1.9-2.014.10.3282.32305956390.1850.3284100
2.01-2.154.10.19242154452580.1080.1926.4100
2.15-2.324.10.1246.12030549390.0690.1249.7100
2.32-2.554.10.0848.71863545180.0470.08412.8100
2.55-2.854.10.05812.51690240950.0320.05816.9100
2.85-3.294.10.04713.11508336440.0260.04721.5100
3.29-4.024.10.04911.91264630610.0260.04927.1100
4.02-5.694.10.03914.5989924000.0220.03929.5100
5.69-33.03740.02423.9523013150.0130.02428.998.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
PHASER2.1.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O5X

1o5x


Resolution: 1.8→73.79 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2646 / WRfactor Rwork: 0.2083 / FOM work R set: 0.7561 / SU B: 4.221 / SU ML: 0.126 / SU R Cruickshank DPI: 0.1526 / SU Rfree: 0.1486 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 2041 5 %RANDOM
Rwork0.2061 ---
obs0.2087 38709 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.17 Å2 / Biso mean: 29.867 Å2 / Biso min: 13.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å2-0 Å20.26 Å2
2---0.35 Å2-0 Å2
3----0.87 Å2
Refinement stepCycle: final / Resolution: 1.8→73.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3526 0 10 273 3809
Biso mean--36.88 43.49 -
Num. residues----479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193600
X-RAY DIFFRACTIONr_bond_other_d0.0020.023343
X-RAY DIFFRACTIONr_angle_refined_deg1.851.9424883
X-RAY DIFFRACTIONr_angle_other_deg1.05437611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7845476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.1225.034149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2115565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1021515
X-RAY DIFFRACTIONr_chiral_restr0.1070.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024183
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02824
X-RAY DIFFRACTIONr_mcbond_it2.9723.0551913
X-RAY DIFFRACTIONr_mcbond_other2.9723.0541912
X-RAY DIFFRACTIONr_mcangle_it3.8784.5662380
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 166 -
Rwork0.32 2804 -
all-2970 -
obs--99.97 %

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