[English] 日本語
Yorodumi
- PDB-4o54: Crystal Structure of Trichomonas vaginalis Triosephosphate Isomer... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4o54
TitleCrystal Structure of Trichomonas vaginalis Triosephosphate Isomerase Ile45-Phe 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: 1.9 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 1.1Mar 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6064
Polymers27,5371
Non-polymers693
Water3,405189
1
A: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2118
Polymers55,0732
Non-polymers1386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545x,-y-1,-z1
Buried area4070 Å2
ΔGint-78 kcal/mol
Surface area18220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.829, 56.202, 105.877
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein Triosephosphate isomerase


Mass: 27536.697 Da / Num. of mol.: 1 / Mutation: I45F
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.: 189 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.38 %
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

-
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: 1.9→46.829 Å / Num. all: 21301 / Num. obs: 21301 / % possible obs: 94.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Biso Wilson estimate: 20 Å2 / Rsym value: 0.052 / Net I/σ(I): 30.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-25.30.272.81460627810.2789.9
2-2.1210.40.1973.92959828500.19792.7
2.12-2.2710.90.1375.62972227380.13794
2.27-2.4510.90.1037.32779625600.10394.6
2.45-2.6910.80.07410.12588923940.07495.5
2.69-310.80.0514.72350821800.0596.2
3-3.4710.70.03519.92110519710.03597
3.47-4.2510.60.0321.31798116960.0397.6
4.25-6.0110.30.02721.91384213500.02798.5
6.01-46.8299.80.02127.376217810.02197

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 31.87 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.83 Å
Translation2.5 Å42.83 Å

-
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: 1.9→46.829 Å / Occupancy max: 1 / Occupancy min: 0.41 / SU ML: 0.18 / σ(F): 0 / Phase error: 19.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2148 1491 7 %random
Rwork0.1654 ---
obs0.1689 21287 94.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.4 Å2 / Biso mean: 21.2225 Å2 / Biso min: 8.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 3 189 2078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151972
X-RAY DIFFRACTIONf_angle_d1.42666
X-RAY DIFFRACTIONf_chiral_restr0.105301
X-RAY DIFFRACTIONf_plane_restr0.007351
X-RAY DIFFRACTIONf_dihedral_angle_d12.389696
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.9640.22471260.18331685181189
1.964-2.03420.25481300.1691714184491
2.0342-2.11560.20861290.15331716184593
2.1156-2.21190.23171340.15291768190293
2.2119-2.32850.20971320.1531764189694
2.3285-2.47440.18341350.16421790192594
2.4744-2.66540.23661360.17411802193895
2.6654-2.93360.23621380.17831836197495
2.9336-3.3580.21411380.17991841197996
3.358-4.23030.18731420.15911881202397
4.2303-46.84360.22341510.15891999215097
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)
10.25140.10050.0190.135-0.09940.15490.0284-0.26660.38480.1786-0.20870.4074-0.2188-0.1852-0.00050.16470.0051-0.00140.1486-0.05280.1635-13.8746-10.474721.575
21.09350.1476-0.29771.0358-0.30531.3-0.02360.0054-0.1063-0.1489-0.02360.20760.1571-0.24860.00040.17090.0032-0.03640.211-0.04870.1844-21.2262-24.514912.6799
30.14240.15910.01340.17740.03780.0641-0.2030.23080.2133-0.260.2171-0.1962-0.3199-0.0397-0.0050.25950.02560.00750.1802-0.04870.2102-10.1861-20.6313-5.4225
40.57220.57590.31571.8676-0.28111.35790.0550.2850.086-0.3573-0.1599-0.3498-0.04650.1391-0.00430.25550.05030.00260.209-0.02140.1689-6.5023-17.61354.441
50.687-0.08870.19420.03610.02110.46410.15130.41940.6852-0.1421-0.1985-0.22050.06840.2812-0.00080.1358-0.00250.00870.2290.0240.30428.1353-17.992818.0429
61.3143-0.51340.61171.01730.52830.7918-0.08280.17080.1589-0.1061-0.0721-0.3762-0.08230.0782-0.00140.1354-0.01830.00540.14820.02510.1557-1.2162-14.747716.0283
71.49620.43410.1060.55450.8581.495-0.0826-0.0527-0.00130.00280.0349-0.2531-0.11660.1561-0.00030.11570.0017-0.02140.1366-0.0020.147-4.0059-10.999522.0418
80.762-0.21-0.06220.1008-0.25391.24820.0228-0.1123-0.10970.0342-0.16370.04790.134-0.122600.1344-0.0008-0.00880.1617-0.03780.144-13.6117-19.00325.399
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 8:64)A8 - 64
3X-RAY DIFFRACTION3(CHAIN A AND RESID 65:83)A65 - 83
4X-RAY DIFFRACTION4(CHAIN A AND RESID 84:123)A84 - 123
5X-RAY DIFFRACTION5(CHAIN A AND RESID 124:145)A124 - 145
6X-RAY DIFFRACTION6(CHAIN A AND RESID 146:182)A146 - 182
7X-RAY DIFFRACTION7(CHAIN A AND RESID 183:219)A183 - 219
8X-RAY DIFFRACTION8(CHAIN A AND RESID 220:252)A220 - 252

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more