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- PDB-4o4v: Crystal Structure of Trichomonas vaginalis Triosephosphate Isomer... -

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Basic information

Entry
Database: PDB / ID: 4o4v
TitleCrystal Structure of Trichomonas vaginalis Triosephosphate Isomerase Tvag_497370 (Ile-45 variant)
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM barrel
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.23 Å
AuthorsLara-Gonzalez, S. / 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. / 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 1.1Feb 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_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_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)27,5493
Polymers27,5031
Non-polymers462
Water5,062281
1
A: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0976
Polymers55,0052
Non-polymers924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area3800 Å2
ΔGint-62 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.220, 56.750, 107.860
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
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.: 281 / 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: 2.63 Å3/Da / Density % sol: 53.18 %
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: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9786 Å
DetectorDetector: CCD / Date: Mar 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.23→23.064 Å / Num. all: 84500 / Num. obs: 84500 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 10.17 Å2 / Rsym value: 0.086 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.23-1.35.60.4891.168709122900.489100
1.3-1.385.60.3391.765290115740.339100
1.38-1.475.70.2392.562040109270.239100
1.47-1.595.70.1643.858275102080.164100
1.59-1.745.70.1035.95401193980.103100
1.74-1.945.80.1015.74929485330.101100
1.94-2.255.80.0817.44393575980.081100
2.25-2.755.80.0639.53719164430.063100
2.75-3.895.40.05910.12687549710.05998.4
3.89-23.0644.50.05311.31148625580.05388.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 34 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å23.06 Å
Translation2.5 Å23.06 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: 1.23→23.064 Å / Occupancy max: 1 / Occupancy min: 0.36 / SU ML: 0.07 / σ(F): 0 / Phase error: 13.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1564 2000 2.37 %random
Rwork0.1455 ---
obs0.1457 84422 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 44.02 Å2 / Biso mean: 13.1018 Å2 / Biso min: 5.8 Å2
Refinement stepCycle: LAST / Resolution: 1.23→23.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 2 281 2148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151960
X-RAY DIFFRACTIONf_angle_d1.4762659
X-RAY DIFFRACTIONf_chiral_restr0.09305
X-RAY DIFFRACTIONf_plane_restr0.009347
X-RAY DIFFRACTIONf_dihedral_angle_d11.444692
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.23-1.26080.18251410.171558295970100
1.2608-1.29480.16921430.159358776020100
1.2948-1.33290.17741410.150657985939100
1.3329-1.3760.17161420.147558716013100
1.376-1.42510.16551430.145958716014100
1.4251-1.48220.15211420.135858686010100
1.4822-1.54960.14261420.129458596001100
1.5496-1.63130.1371430.124759096052100
1.6313-1.73350.13251430.126758716014100
1.7335-1.86730.15391440.133459296073100
1.8673-2.05510.14841440.13659436087100
2.0551-2.35220.13851450.131959676112100
2.3522-2.96250.16711460.149460266172100
2.9625-23.0680.16621410.16635804594593
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)
10.3034-0.01810.11790.14240.17410.5129-0.02870.00630.0031-0.0418-0.04120.008-0.0759-0.0645-0.25260.069-0.0040.01270.0852-0.01570.0812-14.706724.3553-15.2222
20.3226-0.05620.58350.1621-0.54182.3273-0.1162-0.08570.17210.0389-0.03960.1283-0.2898-0.115-0.05750.06210.0076-0.01510.1269-0.04520.1006-25.111130.806-14.8701
30.4395-0.28780.13240.2462-0.13530.15930.1340.2415-0.1056-0.2599-0.13480.06330.0162-0.15870.02640.0886-0.00420.00620.1896-0.04540.1392-25.31717.8901-25.6511
40.0078-0.0472-0.03670.30680.35790.9019-0.03160.0069-0.01790.0655-0.0305-0.00480.0869-0.09170.24130.074-0.01640.01470.0862-0.01920.0734-16.813321.5281-3.9076
50.4024-0.37250.11240.72980.0190.8685-0.0413-0.0305-0.00250.11830.0024-0.10170.06250.0578-0.00340.09490.00050.00830.0845-0.0050.0882-3.841418.5692-4.8061
60.65990.2038-0.18260.41040.20830.8294-0.03990.0018-0.08650.07730.0041-0.09950.13460.07290.05910.08440.00990.01710.07180.00340.09741.23714.809-14.2463
70.11440.145-0.17540.42880.06840.6133-0.06860.0565-0.0036-0.00720.142-0.1312-0.00560.02380.00780.09260.00450.02060.087200.11141.769914.9255-23.6828
80.5457-0.0328-0.0420.29050.43930.6641-0.03310.07850.03420.0049-0.01410.0050.01520.0085-0.02840.0644-0.00760.02110.0777-0.00530.0776-7.513314.5212-22.6421
90.6196-0.20550.02620.43830.1570.8221-0.00690.0920.0622-0.0364-0.0695-0.0243-0.0351-0.0892-0.14680.0765-0.00180.00940.0958-0.01090.0841-13.096321.1661-24.8374
100.1083-0.1993-0.03510.5364-0.05450.17860.02560.1262-0.1389-0.279-0.1159-0.02750.0838-0.0114-0.00460.0989-0.00480.0180.1428-0.03540.097-16.068514.3964-30.598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:17 AND NOT (ELEMENT H))A0
2X-RAY DIFFRACTION2(CHAIN A AND RESID 18:28 AND NOT (ELEMENT H))A0
3X-RAY DIFFRACTION3(CHAIN A AND RESID 29:35 AND NOT (ELEMENT H))A0
4X-RAY DIFFRACTION4(CHAIN A AND RESID 36:87 AND NOT (ELEMENT H))A0
5X-RAY DIFFRACTION5(CHAIN A AND RESID 88:119 AND NOT (ELEMENT H))A0
6X-RAY DIFFRACTION6(CHAIN A AND RESID 120:170 AND NOT (ELEMENT H))A0
7X-RAY DIFFRACTION7(CHAIN A AND RESID 171:197 AND NOT (ELEMENT H))A0
8X-RAY DIFFRACTION8(CHAIN A AND RESID 198:218 AND NOT (ELEMENT H))A0
9X-RAY DIFFRACTION9(CHAIN A AND RESID 219:246 AND NOT (ELEMENT H))A0
10X-RAY DIFFRACTION10(CHAIN A AND RESID 247:251 AND NOT (ELEMENT H))A0

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