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- PDB-1oep: Structure of Trypanosoma brucei enolase reveals the inhibitory di... -

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Basic information

Entry
Database: PDB / ID: 1oep
TitleStructure of Trypanosoma brucei enolase reveals the inhibitory divalent metal site
ComponentsENOLASE
KeywordsLYASE / GLYCOLYSIS / HIS-TAG
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / ciliary plasm / glycolytic process / magnesium ion binding / cytoplasm / cytosol
Similarity search - Function
Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like C-terminal domain ...Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
phosphopyruvate hydratase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDa Silva giotto, M.T. / Navarro, M.V.A.S. / Garratt, R.C. / Rigden, D.J.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The Crystal Structure of Trypanosoma Brucei Enolase: Visualisation of the Inhibitory Metal Binding Site III and Potential as Target for Selective, Irreversible Inhibition
Authors: Da Silva Giotto, M.T. / Hannaert, V. / Vertommen, D. / Navarro, M.V.A.S. / Rider, M.H. / Michels, P.A.M. / Garratt, R.C. / Rigden, D.J.
History
DepositionMar 28, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_label_seq_id / _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: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2907
Polymers46,8761
Non-polymers4136
Water4,306239
1
A: ENOLASE
hetero molecules

A: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,57914
Polymers93,7532
Non-polymers82612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)74.018, 110.536, 109.098
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2076-

HOH

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Components

#1: Protein ENOLASE / 2-PHOSPHOGLYCERATE DEHYDRATASE / 2-PHOSPHO-D-GLYCERATE HYDRO-LYASE


Mass: 46876.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CHAIN A HAS COVALENTLY LINKED 2 VISIBLE RESIDUES IN AN ARTEFACTUAL N-TERMINAL EXTENSION RESULTING FROM CLEAVAGE OF HIS-TAG, RESIDUES -3 TO -1
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NDH8, phosphopyruvate hydratase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYSES THE CONVERSION OF 2-PHOSPHO-D-GLYCERATE TO PHOSPHOENOLPYRUVATE AND WATER. THIS PROTEIN ...CATALYSES THE CONVERSION OF 2-PHOSPHO-D-GLYCERATE TO PHOSPHOENOLPYRUVATE AND WATER. THIS PROTEIN REQUIRES A DIVALENT METAL ION AS A COFACTOR FOR CATALYSIS. EXISTS AS A HOMODIMER.
Sequence detailsTWO ARG RESIDUES ARE MISTRANSLATED AS LYS

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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: 2.38 Å3/Da / Density % sol: 47.92 %
Crystal growpH: 6.5 / Details: 0.01M ZNSO4,0.1 M MES PH 6.5, 25% PEGMME550
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / Details: Hannaert, V., (2003) Eur.J.Biochem., 270, 3205.
Components of the solutions
*PLUS
Conc.: 6 mg/ml / Common name: protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→38.82 Å / Num. obs: 20116 / % possible obs: 99.3 % / Redundancy: 4.7 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 1.9 / % possible all: 93.4
Reflection
*PLUS
Lowest resolution: 38.8 Å / % possible obs: 97.2 % / Rmerge(I) obs: 0.0652
Reflection shell
*PLUS
% possible obs: 93.4 %

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Processing

Software
NameVersionClassification
CNS1refinement
AUTOMARdata reduction
AUTOMARdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ONE

1one


Resolution: 2.3→38.82 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1023 5.1 %RANDOM
Rwork0.21 ---
obs0.21 20116 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.1806 Å2 / ksol: 0.327786 e/Å3
Displacement parametersBiso mean: 43.7 Å2
Baniso -1Baniso -2Baniso -3
1-5.23 Å20 Å20 Å2
2--1.12 Å20 Å2
3----6.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.3→38.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3211 0 19 239 3469
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.651.5
X-RAY DIFFRACTIONc_mcangle_it5.22
X-RAY DIFFRACTIONc_scbond_it5.052
X-RAY DIFFRACTIONc_scangle_it6.972.5
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.337 94 4.9 %
Rwork0.285 1839 -
obs--96.9 %
Refinement
*PLUS
Num. reflection obs: 17334 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
LS refinement shell
*PLUS
Num. reflection Rwork: 1942

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