[English] 日本語
Yorodumi
- PDB-7v8t: Crystal structure of class II pyruvate aldolase from Pseudomonas ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7v8t
TitleCrystal structure of class II pyruvate aldolase from Pseudomonas aeruginosa.
Components2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
KeywordsLYASE / Class II pyruvate aldolase / Hexamer / TIM barrel fold
Function / homology
Function and homology information


: / Lyases; Carbon-carbon lyases; Aldehyde-lyases / phenylacetate catabolic process / metal ion binding
Similarity search - Function
: / 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
IODIDE ION / Hydroxypyruvate/pyruvate aldolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsSeo, P.W. / Kim, J.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018M3D3A1A01055735 Korea, Republic Of
CitationJournal: To Be Published
Title: Biochemical and Molecular Characterization of Pyruvate Aldolase for the Synthesis of 2-Keto-4-hydroxybutyrate.
Authors: Jeong, Y.J. / Le, T.K. / Seo, P.W. / Ju, S.B. / Kim, J.S. / Yeom, S.J.
History
DepositionAug 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
B: 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
C: 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
D: 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
E: 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
F: 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,21518
Polymers169,3816
Non-polymers1,83412
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28640 Å2
ΔGint-143 kcal/mol
Surface area46890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.952, 131.077, 84.202
Angle α, β, γ (deg.)90.000, 106.800, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 2 through 300)
21(chain B and resid 2 through 300)
31(chain C and resid 2 through 300)
41(chain D and (resid 2 through 254 or resid 300))
51(chain E and resid 2 through 300)
61(chain F and resid 2 through 300)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resid 2 through 300)A2 - 300
211(chain B and resid 2 through 300)B2 - 300
311(chain C and resid 2 through 300)C2 - 300
411(chain D and (resid 2 through 254 or resid 300))D0
511(chain E and resid 2 through 300)E2 - 300
611(chain F and resid 2 through 300)F2 - 300

-
Components

#1: Protein
2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase / 2-keto-4-hydroxybutyrate aldolase / 2-keto-3-deoxy-L-rhamnonate aldolase / 4-hydroxy-2-oxo-heptane- ...2-keto-4-hydroxybutyrate aldolase / 2-keto-3-deoxy-L-rhamnonate aldolase / 4-hydroxy-2-oxo-heptane-1 / 7-dioate aldolase / 4-hydroxy-2-oxoheptanedioate aldolase / Pyruvate aldolase


Mass: 28230.148 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A081HJP9, 4-hydroxy-2-oxoheptanedioate aldolase
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 200mM sodium iodide, 24% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. obs: 51389 / % possible obs: 96.6 % / Redundancy: 6 % / Biso Wilson estimate: 39.26 Å2 / Rpim(I) all: 0.094 / Rrim(I) all: 0.241 / Rsym value: 0.173 / Net I/σ(I): 6.4
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 2440 / CC1/2: 0.468 / Rpim(I) all: 0.566 / Rsym value: 0.856

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VWT

2vwt


Resolution: 2.48→46.54 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2267 2050 4 %
Rwork0.186 49224 -
obs0.1876 51274 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.11 Å2 / Biso mean: 42.2375 Å2 / Biso min: 20.45 Å2
Refinement stepCycle: final / Resolution: 2.48→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11346 0 100 317 11763
Biso mean--61.42 40.14 -
Num. residues----1518
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5985X-RAY DIFFRACTION9.91TORSIONAL
12B5985X-RAY DIFFRACTION9.91TORSIONAL
13C5985X-RAY DIFFRACTION9.91TORSIONAL
14D5985X-RAY DIFFRACTION9.91TORSIONAL
15E5985X-RAY DIFFRACTION9.91TORSIONAL
16F5985X-RAY DIFFRACTION9.91TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.48-2.540.28591080.2512590269877
2.54-2.60.30251370.26063274341195
2.6-2.670.31711350.25793248338395
2.67-2.750.31041350.25413269340496
2.75-2.840.27341320.24433206333893
2.84-2.940.25121430.22383403354698
2.94-3.060.2741410.21763380352198
3.06-3.190.24171400.21693376351699
3.19-3.360.25891400.20083359349998
3.36-3.570.22971360.17743254339095
3.57-3.850.2071420.16043430357299
3.85-4.240.22341410.15873380352198
4.24-4.850.17931390.1463332347196
4.85-6.110.21441430.16333406354998
6.11-46.540.15381380.1593317345594
Refinement TLS params.Method: refined / Origin x: -19.1135 Å / Origin y: -19.6095 Å / Origin z: 4.9468 Å
111213212223313233
T0.2355 Å20.0169 Å20.0161 Å2-0.234 Å20.0259 Å2--0.2819 Å2
L0.2079 °20.0235 °20.0134 °2-0.3564 °20.231 °2--0.9784 °2
S-0.0432 Å °0.0158 Å °-0.0109 Å °0.0307 Å °0.0436 Å °0.0619 Å °0.0469 Å °-0.0783 Å °-0.0013 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 300
2X-RAY DIFFRACTION1allA301
3X-RAY DIFFRACTION1allB2 - 300
4X-RAY DIFFRACTION1allB301
5X-RAY DIFFRACTION1allC2 - 300
6X-RAY DIFFRACTION1allC301
7X-RAY DIFFRACTION1allD2 - 254
8X-RAY DIFFRACTION1allD300 - 301
9X-RAY DIFFRACTION1allE2 - 300
10X-RAY DIFFRACTION1allE301
11X-RAY DIFFRACTION1allF2 - 301
12X-RAY DIFFRACTION1allS1 - 317

+
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