[English] 日本語
Yorodumi
- PDB-5tkc: Crystal structure of FBP aldolase from Toxoplasma gondii, ternary... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tkc
TitleCrystal structure of FBP aldolase from Toxoplasma gondii, ternary complex
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / TIM BARREL / ALDOLASE / GLYCOLYSIS / SUBSTRATE / INTERMEDIATE / ENAMINE / COVALENT
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process
Similarity search - Function
Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1,3-DIHYDROXYACETONEPHOSPHATE / GLYCERALDEHYDE-3-PHOSPHATE / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.779 Å
AuthorsHeron, P.W. / Sygusch, J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Isomer activation controls stereospecificity of class I fructose-1,6-bisphosphate aldolases.
Authors: Heron, P.W. / Sygusch, J.
History
DepositionOct 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5794
Polymers39,1471
Non-polymers4323
Water5,783321
1
A: Fructose-bisphosphate aldolase
hetero molecules

A: Fructose-bisphosphate aldolase
hetero molecules

A: Fructose-bisphosphate aldolase
hetero molecules

A: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,31616
Polymers156,5874
Non-polymers1,72912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area15760 Å2
ΔGint-65 kcal/mol
Surface area46670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.848, 109.848, 54.882
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-781-

HOH

21A-791-

HOH

-
Components

#1: Protein Fructose-bisphosphate aldolase /


Mass: 39146.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: ald-1 / Plasmid: pE-SUMO-AMP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Star (DE3) / References: UniProt: Q8I8I2, fructose-bisphosphate aldolase
#2: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE / Dihydroxyacetone phosphate


Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O6P
#3: Chemical ChemComp-G3H / GLYCERALDEHYDE-3-PHOSPHATE / Glyceraldehyde 3-phosphate


Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O6P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Sodium Acetate, 0.2M Lithium Sulfate, 3.5% PEG 8000, 10% PEG 1000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2014
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 31989 / % possible obs: 97.5 % / Redundancy: 13 % / Biso Wilson estimate: 22.61 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.017 / Rrim(I) all: 0.063 / Χ2: 1.098 / Net I/av σ(I): 45.524 / Net I/σ(I): 13.3 / Num. measured all: 417400
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.8190.82812670.8040.2760.8760.90178.8
1.81-1.849.40.66913990.8810.2170.7060.91789
1.84-1.8810.60.53215690.9240.1650.5580.96397.9
1.88-1.9211.40.41516110.960.1260.4351.01498.3
1.92-1.9611.70.36315780.9660.1090.381.06797.5
1.96-211.90.29715770.980.0880.311.01999.7
2-2.0512.30.22115880.9880.0650.2311.00797.7
2.05-2.1112.60.18315910.9920.0530.1911.02398.3
2.11-2.17130.14816290.9950.0420.1540.97599.8
2.17-2.2413.80.1315990.9970.0360.1350.93398.5
2.24-2.3214.10.10716060.9980.0290.1110.93598.7
2.32-2.4214.60.08816040.9990.0240.0910.81499
2.42-2.5314.60.07416070.9990.020.0770.86299.2
2.53-2.6614.60.06716250.9990.0180.070.9199.4
2.66-2.8314.60.05616550.9990.0150.0580.98299.5
2.83-3.0414.50.04816410.9990.0130.051.06699.6
3.04-3.3514.60.04216530.9990.0110.0441.24199.5
3.35-3.8314.40.03816780.9990.010.0391.61799.7
3.83-4.8314.10.032168910.0090.0331.59799.8
4.83-5013.30.03618230.9990.010.0381.75199.8

-
Processing

Software
NameVersionClassification
PHENIXrefinement
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.779→38.837 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1914 1999 6.26 %
Rwork0.152 29949 -
obs0.1545 31948 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.15 Å2 / Biso mean: 32.5523 Å2 / Biso min: 9.65 Å2
Refinement stepCycle: final / Resolution: 1.779→38.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2644 0 42 321 3007
Biso mean--49.74 40.73 -
Num. residues----348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082746
X-RAY DIFFRACTIONf_angle_d0.8283712
X-RAY DIFFRACTIONf_chiral_restr0.051411
X-RAY DIFFRACTIONf_plane_restr0.006484
X-RAY DIFFRACTIONf_dihedral_angle_d14.2631671
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 (%)
1.7794-1.82390.28461130.23631706181980
1.8239-1.87320.26521370.21832050218796
1.8732-1.92830.25951420.21932117225998
1.9283-1.99050.28191410.21192126226798
1.9905-2.06170.24091430.18472136227998
2.0617-2.14420.20141420.17222134227699
2.1442-2.24180.23911450.15322161230699
2.2418-2.360.18191440.1422160230499
2.36-2.50780.18171440.13652159230399
2.5078-2.70140.16191440.13521612305100
2.7014-2.97310.18541470.14852191233899
2.9731-3.40310.18571480.146222252373100
3.4031-4.28670.16491500.126822452395100
4.2867-38.84640.17491590.148123782537100
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)
11.44210.6387-0.14912.13370.73040.9833-0.09530.07260.2204-0.28310.12480.5662-0.2113-0.0492-0.00430.1895-0.0284-0.01160.18630.07520.314-36.20754.0444-4.3289
20.99740.1865-0.05731.4928-0.00030.5895-0.00030.1170.0657-0.13440.04740.1050.0036-0.0340.0050.110.0007-0.01280.14590.02360.0826-18.2573-0.2428-7.5738
30.89230.479-0.28050.92850.60381.5290.01840.2060.0211-0.4281-0.03710.4571-0.0293-0.0599-0.04670.2501-0.0369-0.12690.2010.0460.2858-35.0626-8.844-15.2229
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 100 )A2 - 100
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 277 )A101 - 277
3X-RAY DIFFRACTION3chain 'A' and (resid 278 through 363 )A278 - 363

+
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