[English] 日本語
Yorodumi
- PDB-4fua: L-FUCULOSE-1-PHOSPHATE ALDOLASE COMPLEX WITH PGH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fua
TitleL-FUCULOSE-1-PHOSPHATE ALDOLASE COMPLEX WITH PGH
ComponentsL-FUCULOSE-1-PHOSPHATE ALDOLASE
KeywordsLYASE (ALDEHYDE) / CLASS II ALDOLASE / ZINC ENZYME / HYDROLASE
Function / homology
Function and homology information


D-arabinose catabolic process / L-fuculose-phosphate aldolase / L-fuculose-phosphate aldolase activity / L-fucose catabolic process / pentose catabolic process / aldehyde-lyase activity / zinc ion binding / cytosol
Similarity search - Function
L-fucose phosphate aldolase / L-fuculose-1-phosphate Aldolase / Class II aldolase/adducin N-terminal domain / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / PHOSPHOGLYCOLOHYDROXAMIC ACID / L-fuculose phosphate aldolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.43 Å
AuthorsDreyer, M.K. / Schulz, G.E.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Catalytic mechanism of the metal-dependent fuculose aldolase from Escherichia coli as derived from the structure.
Authors: Dreyer, M.K. / Schulz, G.E.
#1: Journal: To be Published
Title: The Refined High Resolution Structure of the Metal Ion Dependent L-Fuculose-1-Phosphate Aldolase (Class II) from Escherichia Coli
Authors: Dreyer, M.K. / Schulz, G.E.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: The Spatial Structure of the Class II L-Fuculose-1-Phosphate Aldolase from Escherichia Coli
Authors: Dreyer, M.K. / Schulz, G.E.
#3: Journal: Angew.Chem.Int.Ed.Engl. / Year: 1991
Title: Diastereoselective Enzymatic Aldol Additions: L-Rhamnulose and L-Fuculose 1-Phosphate Aldolases from E.Coli
Authors: Fessner, W.-D. / Sinerius, G. / Schneider, A. / Dreyer, M. / Schulz, G.E. / Badia, J. / Aguilar, J.
History
DepositionFeb 14, 1996-
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-FUCULOSE-1-PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2165
Polymers23,8051
Non-polymers4114
Water1,18966
1
A: L-FUCULOSE-1-PHOSPHATE ALDOLASE
hetero molecules

A: L-FUCULOSE-1-PHOSPHATE ALDOLASE
hetero molecules

A: L-FUCULOSE-1-PHOSPHATE ALDOLASE
hetero molecules

A: L-FUCULOSE-1-PHOSPHATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,86420
Polymers95,2214
Non-polymers1,64316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation21_556z,y,-x+11
crystal symmetry operation23_655-z+1,y,x1
Buried area11560 Å2
ΔGint-245 kcal/mol
Surface area30910 Å2
MethodPISA, PQS
2
A: L-FUCULOSE-1-PHOSPHATE ALDOLASE
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)581,183120
Polymers571,32824
Non-polymers9,85696
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_666-y+1,-x+1,-z+11
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation19_666-x+1,-z+1,-y+11
crystal symmetry operation20_565x,-z+1,y1
crystal symmetry operation21_556z,y,-x+11
crystal symmetry operation22_565z,-y+1,x1
crystal symmetry operation23_655-z+1,y,x1
crystal symmetry operation24_666-z+1,-y+1,-x+11
Buried area81480 Å2
ΔGint-1544 kcal/mol
Surface area173290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.600, 183.600, 183.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-300-

SO4

21A-402-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein L-FUCULOSE-1-PHOSPHATE ALDOLASE


Mass: 23805.318 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PGH IS A TRANSITION STATE ANALOGUE INHIBITOR / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 ECL116 / Plasmid: PKKFA2 / Gene (production host): FUCA / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P0AB87, L-fuculose-phosphate aldolase

-
Non-polymers , 5 types, 70 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-PGH / PHOSPHOGLYCOLOHYDROXAMIC ACID


Mass: 171.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6NO6P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.71 Å3/Da / Density % sol: 54 %
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1drop
30.5 mM1dropZnCl2
410 mMbeta-mercaptoethanol1drop
51.62 Mammonium sulfate1reservoir
620 mMpotassium phosphate1reservoir
74 mM1reservoirZnCl2
84 mMbeta-mercaptoethanol1reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.13 Å / Num. obs: 10101 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.073
Reflection
*PLUS
Highest resolution: 2.43 Å / Num. obs: 8744 / % possible obs: 85 % / Num. measured all: 50904
Reflection shell
*PLUS
% possible obs: 47 %

-
Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
XDSdata reduction
X-PLOR3phasing
RefinementResolution: 2.43→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.185 --
obs0.185 8744 85 %
Displacement parametersBiso mean: 18 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati sigma a obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.43→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1593 0 18 66 1677
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.81.5
X-RAY DIFFRACTIONx_mcangle_it2.82
X-RAY DIFFRACTIONx_scbond_it2.52
X-RAY DIFFRACTIONx_scangle_it4.12.5

+
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