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- PDB-2y63: Crystal structure of Leishmanial E65Q-TIM complexed with Bromohyd... -

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Basic information

Entry
Database: PDB / ID: 2y63
TitleCrystal structure of Leishmanial E65Q-TIM complexed with Bromohydroxyacetone phosphate
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE / FATTY ACID BIOSYNTHESIS / TRANSITION STATE ANALOGUE / GLYCOLYSIS / PENTOSE SHUNT / GLUCONEOGENESIS / TIM / GOP / GLYCOSOME / LIPID SYNTHESIS / TRANSITION STATE
Function / homology
Function and homology information


glycosome / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / 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-bromo-2-oxo-propoxy)phosphonic acid / Triosephosphate isomerase
Similarity search - Component
Biological speciesLEISHMANIA MEXICANA (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsVenkatesan, R. / Alahuhta, M. / Pihko, P.M. / Wierenga, R.K.
CitationJournal: Protein Sci. / Year: 2011
Title: High Resolution Crystal Structures of Triosephosphate Isomerase Complexed with its Suicide Inhibitors: The Conformational Flexibility of the Catalytic Glutamate in its Closed, Liganded Active Site.
Authors: Venkatesan, R. / Alahuhta, M. / Pihko, P.M. / Wierenga, R.K.
History
DepositionJan 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.2Dec 20, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4412
Polymers27,2081
Non-polymers2331
Water7,728429
1
A: TRIOSEPHOSPHATE ISOMERASE
hetero molecules

A: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8824
Polymers54,4162
Non-polymers4662
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3540 Å2
ΔGint-15.1 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.880, 50.663, 58.830
Angle α, β, γ (deg.)90.00, 118.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2060-

HOH

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE /


Mass: 27208.236 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: COVALENT LINK BETWEEN A167 AND BBR / Source: (gene. exp.) LEISHMANIA MEXICANA (eukaryote) / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: P48499, triose-phosphate isomerase
#2: Chemical ChemComp-BBR / (3-bromo-2-oxo-propoxy)phosphonic acid


Mass: 232.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6BrO5P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 66 TO GLN
Nonpolymer detailsBROMOHYDROXYACETONE PHOSPHATE IS REPRESENTED BY RESIDUE BBR (SYSTEMATIC NAME: 3-BROMO-2-OXO- ...BROMOHYDROXYACETONE PHOSPHATE IS REPRESENTED BY RESIDUE BBR (SYSTEMATIC NAME: 3-BROMO-2-OXO-PROPOXYPHOSPHONIC ACID) AFTER REACTION AT THE BROMINE ATOM.

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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: 2.3 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 5.5
Details: 21% PEG 6000, 0.1 M SODIUM ACETATE PH 4.5 - 5.5, 1MM DTT, 1MM EDTA, 1MM NAN3.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→99 Å / Num. obs: 18363 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 29.1
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 20.7 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKLdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N55

1n55


Resolution: 1.97→51.99 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.669 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.16956 936 5.1 %RANDOM
Rwork0.13512 ---
obs0.13685 17427 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.611 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å2-0.28 Å2
2---0.11 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.97→51.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 9 429 2338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221987
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.111.9452710
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7965248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.65125.12580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52515344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.848158
X-RAY DIFFRACTIONr_chiral_restr0.0710.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211452
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3071.51250
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.60522040
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2113737
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0974.5670
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.969→2.02 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.18 68 -
Rwork0.146 1282 -
obs--98.83 %
Refinement TLS params.Method: refined / Origin x: 15.1881 Å / Origin y: -0.1817 Å / Origin z: 9.7521 Å
111213212223313233
T0.0081 Å2-0.0012 Å20.0033 Å2-0.0046 Å20.0001 Å2--0.0138 Å2
L0.5114 °2-0.1224 °20.0795 °2-0.2969 °2-0.0524 °2--0.5353 °2
S-0.0315 Å °-0.0111 Å °-0.0351 Å °0.0013 Å °0.0097 Å °-0.0286 Å °0.0254 Å °0.0234 Å °0.0218 Å °

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