[English] 日本語
Yorodumi
- PDB-4pc8: Structure-based protein engineering efforts on the scaffold of a ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pc8
TitleStructure-based protein engineering efforts on the scaffold of a monomeric triosephosphate isomerase yielding a sugar isomerase
ComponentsMa21-TIM
KeywordsISOMERASE / TRIOSEPHOSPHATE ISOMERASE TIM BARREL PROTEIN ENGINEERING SUBSTRATE SPECIFICITY
Function / homology
Function and homology information


glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm
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
GLYCOLIC ACID / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
AuthorsKrause, M. / Neubauer, P. / Wierenga, R.K.
Funding support Germany, Finland, 3items
OrganizationGrant numberCountry
EMBO Shorterm FellowshipASTF 188-2011 Germany
FEBS Shortterm Fellowship Germany
Academy of Finland117874 Finland
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Crystal structures of two monomeric triosephosphate isomerase variants identified via a directed-evolution protocol selecting for L-arabinose isomerase activity.
Authors: Krause, M. / Kiema, T.R. / Neubauer, P. / Wierenga, R.K.
History
DepositionApr 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Data collection / Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / diffrn_source / pdbx_struct_oper_list
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ma21-TIM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8522
Polymers25,7761
Non-polymers761
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.620, 62.620, 136.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-419-

HOH

-
Components

#1: Protein Ma21-TIM


Mass: 25775.514 Da / Num. of mol.: 1 / Mutation: Q65L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: tim / Plasmid: pMK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P04789*PLUS, triose-phosphate isomerase
#2: Chemical ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID / Glycolic acid


Mass: 76.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 21% PEG6000, 100mM citric acid pH5.5, 5% glycerol, 100mM L-arabinose (no further pH adjustment)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.55→56.88 Å / Num. obs: 38092 / % possible obs: 99.9 % / Redundancy: 12.3 % / Net I/σ(I): 23.9
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 1.9 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Coot0.7.1model building
RefinementResolution: 1.55→56.88 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.567 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21649 2007 5 %RANDOM
Rwork0.17331 ---
obs0.17546 38092 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.381 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å2-0 Å2
2--0.56 Å20 Å2
3----1.12 Å2
Refinement stepCycle: 1 / Resolution: 1.55→56.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1815 0 5 320 2140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191874
X-RAY DIFFRACTIONr_bond_other_d0.0010.021830
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.942549
X-RAY DIFFRACTIONr_angle_other_deg0.87934197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8455244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89224.60576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4215314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.919159
X-RAY DIFFRACTIONr_chiral_restr0.1090.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022148
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02423
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3292.536965
X-RAY DIFFRACTIONr_mcbond_other2.3292.538966
X-RAY DIFFRACTIONr_mcangle_it3.3963.7981206
X-RAY DIFFRACTIONr_mcangle_other3.3973.81207
X-RAY DIFFRACTIONr_scbond_it3.5752.975909
X-RAY DIFFRACTIONr_scbond_other3.5732.976910
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5264.2631342
X-RAY DIFFRACTIONr_long_range_B_refined10.96924.0192452
X-RAY DIFFRACTIONr_long_range_B_other10.96824.0272453
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 133 -
Rwork0.264 2759 -
obs--99.69 %

+
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