[English] 日本語
Yorodumi
- PDB-5hjl: Crystal structure of class I tagatose 1,6-bisphosphate aldolase L... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hjl
TitleCrystal structure of class I tagatose 1,6-bisphosphate aldolase LacD from Streptococcus porcinus
ComponentsTagatose 1,6-diphosphate aldolase
KeywordsLYASE / tagatose 1 / 6-bisphosphate aldolase / LacD
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / :
Function and homology information
Biological speciesStreptococcus porcinus str. Jelinkova 176 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsFreichels, R. / Kerff, F. / Herman, R. / Charlier, P. / Galleni, M.
Funding support Belgium, 2items
OrganizationGrant numberCountry
National Fund for Scientific Research Belgium
FRS-FNRSIISN 4.4503 Belgium
CitationJournal: To Be Published
Title: Structure and Characterization of a new class I Tagatose-1,6-bipshosphate aldolase from Streptococcus porcinus : switch in specificity directed by an Arginine
Authors: Freichels, R. / Delmarcelle, M. / Van der Heiden, E. / Herman, R. / Colarusso, A. / Wathelet, B. / Kerff, F. / Galleni, M.
History
DepositionJan 13, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tagatose 1,6-diphosphate aldolase
B: Tagatose 1,6-diphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5028
Polymers73,9262
Non-polymers5766
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-93 kcal/mol
Surface area26990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.660, 93.750, 88.110
Angle α, β, γ (deg.)90.000, 120.580, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 5 - 326 / Label seq-ID: 5 - 326

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

-
Components

#1: Protein Tagatose 1,6-diphosphate aldolase / D-tagatose-1 / 6-bisphosphate aldolase / Tagatose-bisphosphate aldolase


Mass: 36962.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus porcinus str. Jelinkova 176 (bacteria)
Gene: lacD, STRPO_0644 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F3L835, tagatose-bisphosphate aldolase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Small crystals grow in 25% PEG 3350, 0.1M bistris pH 5.5, 0.2 M Ammonium Sulfate. The crystal used for data collection was obtained after micro seeding in the same condition.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.7101 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7101 Å / Relative weight: 1
ReflectionResolution: 3→46.88 Å / Num. obs: 14194 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.296 / Net I/σ(I): 5.9
Reflection shellResolution: 3→3.16 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 2.4 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IV3

3iv3


Resolution: 3→46.87 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2292 710 5 %
Rwork0.1744 16583 -
obs-14194 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.76 Å2 / Biso mean: 61.6768 Å2 / Biso min: 38.61 Å2
Refinement stepCycle: final / Resolution: 3→46.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5016 0 30 8 5054
Biso mean--83.58 55.31 -
Num. residues----644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055134
X-RAY DIFFRACTIONf_angle_d0.9146946
X-RAY DIFFRACTIONf_chiral_restr0.036776
X-RAY DIFFRACTIONf_plane_restr0.006886
X-RAY DIFFRACTIONf_dihedral_angle_d15.1951882
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2936X-RAY DIFFRACTION4.865TORSIONAL
12B2936X-RAY DIFFRACTION4.865TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.23160.31771400.25672670X-RAY DIFFRACTION100
3.2316-3.55670.30111420.21642699X-RAY DIFFRACTION100
3.5567-4.07110.221420.16692688X-RAY DIFFRACTION100
4.0711-5.12810.21131410.14922689X-RAY DIFFRACTION99.9
5.1281-46.88070.18731450.15612738X-RAY DIFFRACTION99.7

+
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://pdbjlvh1.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