[English] 日本語
Yorodumi
- PDB-3ctl: Crystal structure of D-Allulose 6-Phosphate 3-Epimerase from Esch... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ctl
TitleCrystal structure of D-Allulose 6-Phosphate 3-Epimerase from Escherichia coli K12 complexed with D-glucitol 6-phosphate and magnesium
ComponentsD-allulose-6-phosphate 3-epimerase
KeywordsISOMERASE / D-Allulose 6-Phosphate 3-Epimerase / D-glucitol 6-phosphate / (beta/alpha)8 barrel / Carbohydrate metabolism
Function / homology
Function and homology information


allulose 6-phosphate 3-epimerase activity / D-allose catabolic process / Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives / D-ribulose-phosphate 3-epimerase activity / pentose-phosphate shunt, non-oxidative branch / carbohydrate metabolic process / metal ion binding / cytosol
Similarity search - Function
D-allulose-6-phosphate 3-epimerase / Ribulose-phosphate 3-epimerase family signature 2. / Ribulose-phosphate 3-epimerase family signature 1. / Ribulose-phosphate 3-epimerase-like / Ribulose-phosphate 3 epimerase family / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
D-SORBITOL-6-PHOSPHATE / D-allulose-6-phosphate 3-epimerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Chan, K.K. / Gerlt, J.A. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2008
Title: Structural basis for substrate specificity in phosphate binding (beta/alpha)8-barrels: D-allulose 6-phosphate 3-epimerase from Escherichia coli K-12.
Authors: Chan, K.K. / Fedorov, A.A. / Fedorov, E.V. / Almo, S.C. / Gerlt, J.A.
History
DepositionApr 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-allulose-6-phosphate 3-epimerase
B: D-allulose-6-phosphate 3-epimerase
C: D-allulose-6-phosphate 3-epimerase
D: D-allulose-6-phosphate 3-epimerase
E: D-allulose-6-phosphate 3-epimerase
F: D-allulose-6-phosphate 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,56618
Polymers156,8476
Non-polymers1,71912
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17890 Å2
ΔGint-141.3 kcal/mol
Surface area44320 Å2
MethodPISA
2
D: D-allulose-6-phosphate 3-epimerase
F: D-allulose-6-phosphate 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8556
Polymers52,2822
Non-polymers5734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-43.8 kcal/mol
Surface area17070 Å2
MethodPISA
3
B: D-allulose-6-phosphate 3-epimerase
E: D-allulose-6-phosphate 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8556
Polymers52,2822
Non-polymers5734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-43.6 kcal/mol
Surface area17160 Å2
MethodPISA
4
A: D-allulose-6-phosphate 3-epimerase
C: D-allulose-6-phosphate 3-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8556
Polymers52,2822
Non-polymers5734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-43.5 kcal/mol
Surface area17050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.706, 129.040, 154.874
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
D-allulose-6-phosphate 3-epimerase


Mass: 26141.189 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: alsE, yjcU / Production host: Escherichia coli (E. coli)
References: UniProt: P32719, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives
#2: Sugar
ChemComp-S6P / D-SORBITOL-6-PHOSPHATE / 1-O-PHOSPHONO-D-GLUCITOL / D-GLUCITOL-6-PHOSPHATE


Type: D-saccharide / Mass: 262.152 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H15O9P
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 20% PEG 3350, 0.1 M Succinic acid, pH 7.0, VAPOR DIFFUSION, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 3, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. all: 74982 / Num. obs: 74982 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.067

-
Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3CT7

3ct7


Resolution: 2.2→24.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1665519.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 3777 5 %RANDOM
Rwork0.243 ---
obs0.243 74982 96.5 %-
all-74982 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.9587 Å2 / ksol: 0.348849 e/Å3
Displacement parametersBiso mean: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.5 Å20 Å20 Å2
2---6.69 Å20 Å2
3----0.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.2→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10464 0 102 174 10740
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.882
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.692.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.386 353 5 %
Rwork0.379 6689 -
obs--92.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4GPH_par.txtGPH_top.txt
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_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://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