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- PDB-2ptx: Crystal Structure of the T. brucei enolase complexed with sulphat... -

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Basic information

Entry
Database: PDB / ID: 2ptx
TitleCrystal Structure of the T. brucei enolase complexed with sulphate in closed conformation
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 (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNavarro, M.V.A.S. / Rigden, D.J. / Garratt, R.C. / Dias, S.M.G.
Citation
Journal: Febs J. / Year: 2007
Title: Structural flexibility in Trypanosoma brucei enolase revealed by X-ray crystallography and molecular dynamics.
Authors: Navarro, M.V. / Gomes Dias, S.M. / Mello, L.V. / da Silva Giotto, M.T. / Gavalda, S. / Blonski, C. / Garratt, R.C. / Rigden, D.J.
#1: Journal: 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
DepositionMay 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)47,3808
Polymers46,9041
Non-polymers4757
Water6,882382
1
A: Enolase
hetero molecules

A: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,75916
Polymers93,8092
Non-polymers95014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
Length a, b, c (Å)74.773, 111.175, 108.983
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-836-

HOH

DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations: -x, y, -z+1/2

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Components

#1: Protein Enolase / 2-phospho-D-glycerate hydro-lyase


Mass: 46904.434 Da / Num. of mol.: 1 / Mutation: R28K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q38BV6, 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.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 % (w/v) PEG1000, 0.01 M ZnSO4 or ZnCl2, and 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 1, 2004 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→26.1 Å / Num. all: 36178 / Num. obs: 35765 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5019 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OEP

1oep


Resolution: 1.9→26.06 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.38 / SU ML: 0.086 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.142 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20654 4764 5 %RANDOM
Rwork0.16624 ---
all0.16824 34321 --
obs0.16824 33961 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.638 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→26.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 23 382 3711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223385
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9754572
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7455440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.95824.752141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02715603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9091519
X-RAY DIFFRACTIONr_chiral_restr0.0890.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022527
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.21698
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22298
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2333
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5681.52229
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.86823449
X-RAY DIFFRACTIONr_scbond_it1.60831320
X-RAY DIFFRACTIONr_scangle_it2.5574.51118
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→2.002 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.338 231 -
Rwork0.238 4764 -
obs--96.3 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.92230.1829-0.20790.7488-0.4981.652-0.04840.06-0.1192-0.05930.08190.09680.2067-0.2642-0.0335-0.1042-0.0405-0.0086-0.08680.0121-0.076823.2113-20.896420.4224
21.17080.394-0.26931.3684-0.49481.6032-0.03910.0789-0.0052-0.03090.05860.11510.0568-0.2094-0.0195-0.0707-0.0076-0.0152-0.01910.0082-0.013423.9906-18.311219.7651
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-1 - 4292 - 432
3X-RAY DIFFRACTION2AI704 - 10851 - 382

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