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- PDB-4gnj: Crystal Structure Analysis of Leishmania siamensis Triosephosphat... -

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Basic information

Entry
Database: PDB / ID: 4gnj
TitleCrystal Structure Analysis of Leishmania siamensis Triosephosphate Isomerase
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / Tim Barrel
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm
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
ARSENIC / Triosephosphate isomerase
Similarity search - Component
Biological speciesLeishmania sp. siamensis (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsKuaprasert, B. / Riangrungroj, P. / Pornthanakasem, W. / Suginta, W. / Mungthin, M. / Leelayoova, S. / Leartsakulpanich, U.
CitationJournal: To be Published
Title: Crystal Structure Analysis of Leishmania siamensis Triosephosphate Isomerase
Authors: Kuaprasert, B. / Riangrungroj, P. / Pornthanakasem, W. / Suginta, W. / Mungthin, M. / Leelayoova, S. / Leartsakulpanich, U.
History
DepositionAug 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 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_conn_angle / struct_conn / 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 / _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.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_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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,6625
Polymers58,4892
Non-polymers1733
Water6,575365
1
A: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6394
Polymers58,4892
Non-polymers1502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3160 Å2
ΔGint-31 kcal/mol
Surface area18980 Å2
MethodPISA
2
B: Triosephosphate isomerase
hetero molecules

B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6856
Polymers58,4892
Non-polymers1964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3360 Å2
ΔGint-41 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.580, 78.790, 83.160
Angle α, β, γ (deg.)90.00, 101.15, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Triosephosphate isomerase /


Mass: 29244.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania sp. siamensis (eukaryote) / Strain: isolate PCM2 / Gene: Lstim, tim / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I2APN2, triose-phosphate isomerase
#2: Chemical ChemComp-ARS / ARSENIC / Arsenic


Mass: 74.922 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: As
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.18 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 6.5
Details: 0.20M calcium acetate, 0.10M sodium cacodylate trihydrate, 18% PEG 8000, pH 6.5, MICROBATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: RAYONIX SX-165mm / Detector: CCD / Date: Mar 9, 2011 / Details: HELIOS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→81.6 Å / Num. obs: 35257 / % possible obs: 93.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.202 / Net I/σ(I): 14.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.93-2.033.10.2023.8154500.20290.2
2.03-2.163.20.1315.8150970.13191.5
2.16-2.313.30.1345.1147930.13492.6
2.31-2.493.40.0819.3143870.08193.2
2.49-2.733.40.06511.4135420.06594.6
2.73-3.053.40.05213.7124480.05294.9
3.05-3.523.40.03815.9110530.03896.3
3.52-4.323.40.03616.793990.03496.8
4.32-6.13.40.03216.973030.03197.7
6.1-81.63.30.02817.239410.02895.9

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AMK

1amk


Resolution: 1.93→21.61 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.887 / SU ML: 0.075 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.032 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19932 1793 5.1 %RANDOM
Rwork0.15132 ---
all0.15373 ---
obs0.15373 33449 93.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.209 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20.29 Å2
2--0.52 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.93→21.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3749 0 3 365 4117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223920
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.9485350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0835515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.69825.29155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95815669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7241514
X-RAY DIFFRACTIONr_chiral_restr0.0910.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212924
X-RAY DIFFRACTIONr_mcbond_it0.561.52504
X-RAY DIFFRACTIONr_mcangle_it0.98224056
X-RAY DIFFRACTIONr_scbond_it1.83731416
X-RAY DIFFRACTIONr_scangle_it3.0214.51287
LS refinement shellHighest resolution: 1.93 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.19932 1793 -
Rwork0.15132 2310 -
obs-33449 93.23 %
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)
10.779-0.1556-0.10641.0561-0.28880.987-0.0223-0.067-0.06060.0809-0.00850.06550.0196-0.03630.03090.0423-0.0064-0.00810.0568-0.00330.0649-3.4116-0.052417.4237
20.93930.29840.17710.77860.38291.1834-0.05610.182-0.0137-0.13690.0486-0.0229-0.01830.01990.00750.0464-0.004-0.00440.07070.00080.0756.55939.535423.804
32.4529-1.2163-0.17130.8519-0.51561.4380.08060.2045-0.1396-0.1275-0.00350.12760.2088-0.1627-0.07710.11410.05230.04540.30870.19540.16212.570343.910118.195
40000000000000000.00520.0164-0.01580.0405-0.02960.036-13.643626.522113.5236
50.07870.05810.09010.59610.38390.2847-0.010.0264-0.0086-0.0193-0.00320.0147-0.0199-0.01740.01320.1624-0.00350.00760.22270.01260.20481.54220.053720.9274
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 251
2X-RAY DIFFRACTION2B4 - 251
3X-RAY DIFFRACTION3A301
4X-RAY DIFFRACTION3B301
5X-RAY DIFFRACTION4B302
6X-RAY DIFFRACTION5A401 - 582
7X-RAY DIFFRACTION5B401 - 583

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