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- PDB-4o52: Crystal Structure of Trichomonas vaginalis Triosephosphate Isomer... -

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Basic information

Entry
Database: PDB / ID: 4o52
TitleCrystal Structure of Trichomonas vaginalis Triosephosphate Isomerase Ile45-Val mutant (Tvag_497370)
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM barrel
Function / homology
Function and homology information


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
Triosephosphate isomerase
Similarity search - Component
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsLara-Gonzalez, S. / Montero-Moran, G.M. / Benitez-Cardoza, C.G. / Brieba, L.G.
CitationJournal: To be Published
Title: Engineering mutants with altered dimer-monomer equilibrium reveal the existence of stable monomeric Triosephosphate isomerases
Authors: Lara-Gonzalez, S. / Montero-Moran, G.M. / Benitez-Cardoza, C.G. / Brieba, L.G.
History
DepositionDec 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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

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Assembly

Deposited unit
A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5353
Polymers27,4891
Non-polymers462
Water3,459192
1
A: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0696
Polymers54,9772
Non-polymers924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area3800 Å2
ΔGint-64 kcal/mol
Surface area18000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.806, 55.858, 104.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Triosephosphate isomerase


Mass: 27488.654 Da / Num. of mol.: 1 / Mutation: I45V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_497370 / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star rossetaII / References: UniProt: A2EGX9, triose-phosphate isomerase
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M Ammonium acetate, 0.1M Sodium citrate, 30% PEG 4000, pH 5.6, vapor diffusion, hanging drop, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5419 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.95→55.858 Å / Num. all: 20768 / Num. obs: 20768 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 15.34 Å2 / Rsym value: 0.098 / Net I/σ(I): 15.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.95-2.0670.3712.12094229720.371100
2.06-2.187.20.2752.81998227830.275100
2.18-2.337.20.1983.91947627040.198100
2.33-2.527.30.1624.71788924640.162100
2.52-2.767.30.1216.31664822950.121100
2.76-3.087.30.0848.71521420810.084100
3.08-3.567.30.05812.51349918540.058100
3.56-4.367.20.04614.31152915930.046100
4.36-6.177.10.04313.4900512670.043100
6.17-55.8586.50.0413.249137550.0499.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.16 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å55.86 Å
Translation2.5 Å49.31 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.1.4phasing
PHENIXdev_1396refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→49.308 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.21 / σ(F): 0 / Phase error: 18.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2091 1035 4.99 %random
Rwork0.1671 ---
obs0.1692 20724 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.44 Å2 / Biso mean: 13.7191 Å2 / Biso min: 5.42 Å2
Refinement stepCycle: LAST / Resolution: 1.95→49.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 2 192 2060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171915
X-RAY DIFFRACTIONf_angle_d1.4442591
X-RAY DIFFRACTIONf_chiral_restr0.099297
X-RAY DIFFRACTIONf_plane_restr0.007339
X-RAY DIFFRACTIONf_dihedral_angle_d12.142668
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.95-2.05280.24441430.187927412884
2.0528-2.18140.24061440.169327482892
2.1814-2.34990.21911480.155227992947
2.3499-2.58630.22891460.172627782924
2.5863-2.96050.23631480.176528122960
2.9605-3.72980.20251490.163628322981
3.7298-49.32350.16661570.160129793136
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)
10.37980.04090.00160.05240.1260.32810.00650.0647-0.0104-0.1053-0.1356-0.18240.10170.0977-0.00070.09350.00560.00680.11560.02030.1066-8.45654.4676-15.0627
20.0764-0.174-0.34160.40030.78551.5427-0.06790.2304-0.22060.1583-0.0119-0.04750.27530.1429-0.01110.11110.00870.01930.19320.02830.18351.9222-2.0818-14.2828
33.1963-1.2042-1.11650.5129-0.04194.00180.28510.62530.3635-0.1495-0.0755-0.0147-0.32610.19690.52450.1248-0.0249-0.02340.27010.06820.20221.689112.0436-25.0934
40.09290.00690.12880.2724-0.36550.69530.00160.03840.03240.0513-0.0576-0.0616-0.06650.18270.00140.1094-0.0174-0.00560.09630.02140.111-6.5667.192-3.5566
50.3807-0.3992-0.04340.635-0.21321.0493-0.0298-0.09170.01350.0939-0.05990.0088-0.1163-0.0262-0.00110.1093-0.003-0.00960.0934-0.00230.0867-18.597210.7202-4.8348
61.0665-0.09461.05080.20560.30212.2499-0.075-0.10210.01270.1251-0.01530.0136-0.0793-0.2809-0.06150.0832-0.0238-0.01050.13740.01680.0796-30.19387.1326-18.0833
70.4652-0.13680.62570.4206-0.4951.0957-0.15680.01520.22750.16920.14090.1414-0.1892-0.20710.05520.12270.02910.02550.17490.00040.2181-31.623614.3663-15.1801
80.49960.1644-0.34970.37190.07920.417-0.0180.0310.00360.11640.0601-0.0033-0.1284-0.03750.00550.14840.0054-0.03440.0559-0.0030.1024-19.651817.1407-11.9265
90.28740.2746-0.11520.3352-0.16430.2507-0.18930.1775-0.0351-0.04220.1970.06590.0324-0.03980.01280.13620.00540.00320.14470.01790.1391-24.7968.2244-25.9833
100.62810.1133-0.01060.3825-0.57471.0481-0.01570.11970.05330.0119-0.0261-0.0128-0.1301-0.00330.00030.0972-0.0001-0.0160.12690.01250.1159-17.286915.6889-22.3018
110.5026-0.305-0.24940.51380.08540.1372-0.05870.47950.0593-0.3473-0.2329-0.15650.22090.0128-0.11230.16690.0430.03070.24580.03320.105-4.9541.4459-22.891
121.19270.7099-0.13851.05340.23720.2807-0.04620.13750.242-0.17980.0570.04710.01070.0921-0.35070.0866-0.01630.00250.20780.06730.1154-6.816313.4116-28.6089
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:17)A2 - 17
2X-RAY DIFFRACTION2(CHAIN A AND RESID 18:28)A18 - 28
3X-RAY DIFFRACTION3(CHAIN A AND RESID 29:35)A29 - 35
4X-RAY DIFFRACTION4(CHAIN A AND RESID 36:87)A36 - 87
5X-RAY DIFFRACTION5(CHAIN A AND RESID 88:124)A88 - 124
6X-RAY DIFFRACTION6(CHAIN A AND RESID 125:133)A125 - 133
7X-RAY DIFFRACTION7(CHAIN A AND RESID 134:149)A134 - 149
8X-RAY DIFFRACTION8(CHAIN A AND RESID 150:169)A150 - 169
9X-RAY DIFFRACTION9(CHAIN A AND RESID 170:187)A170 - 187
10X-RAY DIFFRACTION10(CHAIN A AND RESID 188:235)A188 - 235
11X-RAY DIFFRACTION11(CHAIN A AND RESID 236:243)A236 - 243
12X-RAY DIFFRACTION12(CHAIN A AND RESID 244:252)A244 - 252

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