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- PDB-4o53: Crystal Structure of Trichomonas vaginalis Triosephosphate Isomer... -

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Basic information

Entry
Database: PDB / ID: 4o53
TitleCrystal Structure of Trichomonas vaginalis Triosephosphate Isomerase Ile45-Leu 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: 2 Å
AuthorsLara-Gonzalez, S. / Montero-Moran, G.M. / Estrella-Hernandez, P. / 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. / Estrella-Hernandez, P. / 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.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_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)27,5724
Polymers27,5031
Non-polymers693
Water3,261181
1
A: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1438
Polymers55,0052
Non-polymers1386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area4080 Å2
ΔGint-77 kcal/mol
Surface area18160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.891, 55.954, 105.157
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: 27502.680 Da / Num. of mol.: 1 / Mutation: I45L
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.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Calcium acetate, 0.1M Sodium cacodylate, 18% PEG 8000, pH 6.5, 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: 2→55.954 Å / Num. all: 19121 / Num. obs: 19121 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 16.93 Å2 / Rsym value: 0.057 / Net I/σ(I): 18.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.114.70.1514.71260926600.15196.6
2.11-2.245.30.1146.41385526030.11498.6
2.24-2.395.30.0947.51293424230.09499
2.39-2.585.30.0838.41226922940.08399.3
2.58-2.835.30.06610.31134621290.06699.6
2.83-3.165.40.05312.71042019430.05399.8
3.16-3.655.30.04314.9924417390.04399.9
3.65-4.475.30.0415776114730.04100
4.47-6.325.20.03914.5611411770.03999.8
6.32-55.9544.90.0411.233036800.0498

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 30.58 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å55.95 Å
Translation2.5 Å49.4 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: 2→49.396 Å / Occupancy max: 1 / Occupancy min: 0.42 / SU ML: 0.19 / σ(F): 0 / Phase error: 19.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 1147 6.01 %random
Rwork0.1646 ---
obs0.1679 19099 98.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.76 Å2 / Biso mean: 17.2255 Å2 / Biso min: 7.25 Å2
Refinement stepCycle: LAST / Resolution: 2→49.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 3 181 2059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141935
X-RAY DIFFRACTIONf_angle_d1.3342611
X-RAY DIFFRACTIONf_chiral_restr0.088298
X-RAY DIFFRACTIONf_plane_restr0.007341
X-RAY DIFFRACTIONf_dihedral_angle_d12.291680
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0910.23511370.16542141227896
2.091-2.20130.23141390.15642184232398
2.2013-2.33920.22581420.15052219236198
2.3392-2.51980.23641410.16732212235399
2.5198-2.77340.251430.17152240238399
2.7734-3.17460.21971450.175522602405100
3.1746-3.99940.18821460.165923042450100
3.9994-49.41120.21761540.162392254699
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)
10.2786-0.0674-0.17420.1333-0.19360.53930.03740.05070.0085-0.0561-0.26730.254-0.0728-0.1609-0.0020.12160.0065-0.01410.1797-0.04320.1458-14.973623.544-15.0934
20.16790.0430.02050.1637-0.11310.1013-0.09130.33440.2638-0.0686-0.01560.062-0.1716-0.1418-0.00010.16230.052-0.00750.23370.00280.1985-25.01331.5342-13.591
30.0356-0.04860.10460.0881-0.18730.43140.03420.2321-0.2759-0.0295-0.02390.27370.3448-0.25840.00570.17640.008-0.03310.3262-0.090.2392-25.879718.1364-23.3363
40.1647-0.1069-0.03120.42610.50460.7857-0.02310.10060.0040.1008-0.05320.08460.057-0.1140.00040.1203-0.01180.0140.1197-0.020.1188-14.918920.7197-4.56
50.3942-0.09690.26370.44810.24380.5882-0.1511-0.00690.12360.05340.0868-0.2020.15350.107-0.0010.18180.01230.01210.14120.00140.1562-1.901816.8611-1.8309
60.22890.03550.35640.24240.16610.60340.0394-0.0912-0.1470.0771-0.0808-0.03140.04270.07970.00010.13190.0035-0.01530.1482-0.02110.14040.038617.6113-13.7628
70.2958-0.179-0.55290.16840.44041.213-0.17730.1852-0.3830.10690.1979-0.07840.21930.27860.02710.16440.0181-0.00860.239-0.02930.31128.245713.7399-15.6443
80.7824-0.06430.16640.66180.6280.7683-0.07910.0817-0.05480.05140.0784-0.08080.09830.02670.00060.14040.01940.00970.1105-0.02330.1486-0.983413.0395-18.1364
90.2169-0.16360.30980.1295-0.1730.8555-0.1989-0.1984-0.20660.22150.22190.05340.52610.10040.03910.25630.02570.04730.1489-0.00340.2006-4.68381.5963-16.3215
100.14530.1020.00190.06260.00950.2621-0.06410.2170.0097-0.0485-0.04670.0115-0.0362-0.02730.00010.12220.01720.00280.1655-0.00020.1562-9.57619.4391-24.8531
110.60680.56340.05280.65610.23250.26470.00710.30060.163-0.3705-0.07220.3092-0.31710.30540.01270.20760.0178-0.02890.2437-0.05360.1531-19.075125.8118-24.4343
120.0279-0.10870.13110.4681-0.55120.65410.01330.2346-0.2049-0.21130.0861-0.03850.1953-0.18350.04950.1036-0.03530.00750.224-0.08030.1241-16.576914.6371-28.7032
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 18:26)A18 - 26
3X-RAY DIFFRACTION3(CHAIN A AND RESID 27:35)A27 - 35
4X-RAY DIFFRACTION4(CHAIN A AND RESID 36:98)A36 - 98
5X-RAY DIFFRACTION5(CHAIN A AND RESID 99:118)A99 - 118
6X-RAY DIFFRACTION6(CHAIN A AND RESID 119:133)A119 - 133
7X-RAY DIFFRACTION7(CHAIN A AND RESID 134:149)A134 - 149
8X-RAY DIFFRACTION8(CHAIN A AND RESID 150:195)A150 - 195
9X-RAY DIFFRACTION9(CHAIN A AND RESID 196:206)A196 - 206
10X-RAY DIFFRACTION10(CHAIN A AND RESID 207:237)A207 - 237
11X-RAY DIFFRACTION11(CHAIN A AND RESID 238:243)A238 - 243
12X-RAY DIFFRACTION12(CHAIN A AND RESID 244:252)A244 - 252

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