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- PDB-4rcx: Trichomonas vaginalis triosephosphate isomerase TVAG_497370 gene ... -

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Basic information

Entry
Database: PDB / ID: 4rcx
TitleTrichomonas vaginalis triosephosphate isomerase TVAG_497370 gene (Ile-45 variant) loop 3 deletion protein
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLara-Gonzalez, S. / Jimenez-Sandoval, P. / Estrella-Hernandez, P. / Brieba, L.G.
CitationJournal: To be Published
Title: Trichomonas vaginalis triosephosphate isomerase loop 3 deletion protein
Authors: Lara-Gonzalez, S. / Jimenez-Sandoval, P. / Estrella-Hernandez, P. / Brieba, L.G.
History
DepositionSep 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: 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_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_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_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_comp_id / _struct_conn.ptnr1_label_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2132
Polymers27,1901
Non-polymers231
Water2,522140
1
A: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4274
Polymers54,3812
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area1720 Å2
ΔGint-42 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.970, 56.730, 105.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Triosephosphate isomerase /


Mass: 27190.340 Da / Num. of mol.: 1 / Mutation: loop 3 deletion, delta(72-77)
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(DE3) / References: UniProt: A2EGX9, triose-phosphate isomerase
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.59 Å3/Da / Density % sol: 52.57 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Calcium acetate, 0.1 M 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-G / Wavelength: 0.98 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→29.963 Å / Num. all: 29120 / Num. obs: 29120 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 22.04 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.2

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: dev_1730)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→29.96 Å / SU ML: 0.16 / σ(F): 0 / σ(I): 2 / Phase error: 18.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2029 1746 6 %RANDOM
Rwork0.1729 ---
obs0.1747 29090 99.35 %-
all-29090 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 1 140 1867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161804
X-RAY DIFFRACTIONf_angle_d1.6262452
X-RAY DIFFRACTIONf_dihedral_angle_d11.286631
X-RAY DIFFRACTIONf_chiral_restr0.091283
X-RAY DIFFRACTIONf_plane_restr0.008320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.75-1.80150.27221440.195222482392100
1.8015-1.85960.24221420.183122482390100
1.8596-1.92610.21451460.175822702416100
1.9261-2.00320.19361430.175222432386100
2.0032-2.09430.20191450.169722642409100
2.0943-2.20470.24571450.169322732418100
2.2047-2.34280.2361460.169322872433100
2.3428-2.52360.20511450.182722772422100
2.5236-2.77740.19531470.180322962443100
2.7774-3.17890.24011470.18523222469100
3.1789-4.00360.18291490.162423242473100
4.0036-29.96760.1691470.16682292243993
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)
14.9064-1.88131.49320.7644-0.43752.03120.00070.1115-0.39570.1537-0.0640.36930.1355-0.03340.93450.1307-0.00710.06720.1356-0.02120.1779-13.667510.6846-20.9597
21.8205-0.070.37030.7753-1.15411.77290.06370.00570.09570.1307-0.0192-0.0533-0.4251-0.14830.00020.23190.00280.04090.232-0.02660.3127-21.391827.694-15.7882
30.83080.0046-0.77861.7799-0.18180.97490.0064-0.2550.05670.3813-0.1416-0.03940.0532-0.1316-0.02310.2113-0.02780.05550.2069-0.07340.2103-19.005121.6162-8.7404
40.6631-0.86780.10821.22970.23241.46690.0462-0.00910.27520.11150.0143-0.1098-0.07460.17050.00120.3402-0.08130.07240.2839-0.05340.2727-11.065119.1038-3.8455
50.6774-0.49250.50170.4438-0.27220.4718-0.2257-0.18880.03670.45290.0622-0.0761-0.23110.061-0.23080.5284-0.0708-0.02840.47570.09120.1619-5.886611.3722-0.786
60.2948-0.1217-0.1230.17930.15090.29670.1171-0.20640.01250.1351-0.0303-0.16220.05330.1322-00.1955-0.01880.00530.2739-0.00450.20622.816918.5157-15.4463
70.91780.17940.07440.57250.18440.84410.0839-0.3646-0.28110.3612-0.1196-0.3290.13260.21270.01240.22990.0186-0.02330.23550.08410.25611.048810.22-13.1608
80.79710.698-0.09190.664-0.31311.0288-0.042-0.00940.0195-0.18680.1644-0.277-0.14530.06210.00020.2246-0.00480.02070.2137-0.00990.24582.099717.003-24.1312
92.41330.3488-0.28580.70351.17342.294-0.00240.0393-0.0443-0.0144-0.0418-0.01510.10680.155600.11370.00080.03170.16950.00270.1452-6.266411.5934-22.4117
101.75410.5514-0.1340.5026-0.23622.01030.05850.19690.1938-0.077-0.12680.042-0.1082-0.1097-0.00030.1895-0.00280.02160.2023-0.01380.1991-13.862919.24-24.7477
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:7 )A1 - 7
2X-RAY DIFFRACTION2( CHAIN A AND RESID 8:35 )A8 - 35
3X-RAY DIFFRACTION3( CHAIN A AND RESID 36:67 )A36 - 67
4X-RAY DIFFRACTION4( CHAIN A AND RESID 72:93 )A72 - 93
5X-RAY DIFFRACTION5( CHAIN A AND RESID 101:114 )A101 - 114
6X-RAY DIFFRACTION6( CHAIN A AND RESID 115:127 )A115 - 127
7X-RAY DIFFRACTION7( CHAIN A AND RESID 128:160 )A128 - 160
8X-RAY DIFFRACTION8( CHAIN A AND RESID 161:186 )A161 - 186
9X-RAY DIFFRACTION9( CHAIN A AND RESID 187:217 )A187 - 217
10X-RAY DIFFRACTION10( CHAIN A AND RESID 218:246 )A218 - 246

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