[English] 日本語
Yorodumi
- PDB-3c3j: Crystal structure of tagatose-6-phosphate ketose/aldose isomerase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c3j
TitleCrystal structure of tagatose-6-phosphate ketose/aldose isomerase from Escherichia coli
ComponentsPutative tagatose-6-phosphate ketose/aldose isomerase
KeywordsISOMERASE / tagatose-6-phosphate ketose/aldose isomerase / structural genomics / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In other compounds / carbohydrate derivative metabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / carbohydrate derivative binding / plasma membrane => GO:0005886 / isomerase activity / hydrolase activity
Similarity search - Function
Sugar isomerase, AgaS / AgaS, SIS domain / GlmS/AgaS, SIS domain 1 / SIS domain / SIS domain / SIS domain profile. / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative D-galactosamine-6-phosphate deaminase AgaS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsZhang, R. / Skarina, T. / Egorova, O. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the tagatose-6-phosphate ketose/aldose isomerase from Escherichia coli.
Authors: Zhang, R. / Skarina, T. / Egorova, O. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionJan 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative tagatose-6-phosphate ketose/aldose isomerase
B: Putative tagatose-6-phosphate ketose/aldose isomerase
C: Putative tagatose-6-phosphate ketose/aldose isomerase
D: Putative tagatose-6-phosphate ketose/aldose isomerase
E: Putative tagatose-6-phosphate ketose/aldose isomerase
F: Putative tagatose-6-phosphate ketose/aldose isomerase


Theoretical massNumber of molelcules
Total (without water)253,7246
Polymers253,7246
Non-polymers00
Water41,3262294
1
A: Putative tagatose-6-phosphate ketose/aldose isomerase
B: Putative tagatose-6-phosphate ketose/aldose isomerase


Theoretical massNumber of molelcules
Total (without water)84,5752
Polymers84,5752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
MethodPISA
2
C: Putative tagatose-6-phosphate ketose/aldose isomerase
D: Putative tagatose-6-phosphate ketose/aldose isomerase


Theoretical massNumber of molelcules
Total (without water)84,5752
Polymers84,5752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
MethodPISA
3
E: Putative tagatose-6-phosphate ketose/aldose isomerase
F: Putative tagatose-6-phosphate ketose/aldose isomerase


Theoretical massNumber of molelcules
Total (without water)84,5752
Polymers84,5752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.941, 81.211, 138.325
Angle α, β, γ (deg.)90.00, 90.21, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Putative tagatose-6-phosphate ketose/aldose isomerase


Mass: 42287.254 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: agaS, yraB, b3136, JW3105 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P42907
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2294 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.2M di-Ammonium citrate, 2.5 mM Glucose-6-phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2006 / Details: Mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→138.68 Å / Num. all: 196168 / Num. obs: 195226 / % possible obs: 99.52 % / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 17.81
Reflection shellResolution: 1.8→1.848 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.9 / Num. unique all: 15168 / % possible all: 97.17

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→47.46 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.95 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.235 / ESU R Free: 0.107
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18512 10357 5 %RANDOM
Rwork0.13597 ---
all0.13844 195226 --
obs0.13844 195226 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20.07 Å2
2--0.49 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16991 0 0 2294 19285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02217410
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211421
X-RAY DIFFRACTIONr_angle_refined_deg1.391.95123762
X-RAY DIFFRACTIONr_angle_other_deg0.999327838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65552201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33723.668758
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.008152648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.53515108
X-RAY DIFFRACTIONr_chiral_restr0.1090.22717
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023558
X-RAY DIFFRACTIONr_nbd_refined0.2270.24150
X-RAY DIFFRACTIONr_nbd_other0.2060.212522
X-RAY DIFFRACTIONr_nbtor_refined0.1760.28670
X-RAY DIFFRACTIONr_nbtor_other0.0880.28488
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.21694
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.267
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3150.2150
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.2104
X-RAY DIFFRACTIONr_mcbond_it1.4221.513499
X-RAY DIFFRACTIONr_mcbond_other0.5351.54415
X-RAY DIFFRACTIONr_mcangle_it1.698217817
X-RAY DIFFRACTIONr_scbond_it3.22137106
X-RAY DIFFRACTIONr_scangle_it4.3454.55945
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 787 -
Rwork0.185 13952 -
obs-15168 97.17 %
Refinement TLS params.Method: refined / Origin x: 16.328 Å / Origin y: 37.851 Å / Origin z: 103.762 Å
111213212223313233
T-0.0012 Å2-0.0054 Å2-0.0089 Å2--0.0113 Å2-0.0038 Å2---0.0039 Å2
L0.055 °2-0.0154 °2-0.0297 °2-0.0122 °2-0.0035 °2--0.0338 °2
S-0.0038 Å °-0.0053 Å °0.002 Å °-0.0042 Å °0.0022 Å °-0.0019 Å °0.0021 Å °-0.0016 Å °0.0016 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1004 - 100
2X-RAY DIFFRACTION1AA101 - 200101 - 200
3X-RAY DIFFRACTION1AA201 - 300201 - 300
4X-RAY DIFFRACTION1AA301 - 364301 - 364
5X-RAY DIFFRACTION1AA376 - 384376 - 384
6X-RAY DIFFRACTION1BB5 - 1005 - 100
7X-RAY DIFFRACTION1BB101 - 200101 - 200
8X-RAY DIFFRACTION1BB201 - 300201 - 300
9X-RAY DIFFRACTION1BB301 - 364301 - 364
10X-RAY DIFFRACTION1BB376 - 383376 - 383
11X-RAY DIFFRACTION1CC5 - 1005 - 100
12X-RAY DIFFRACTION1CC101 - 200101 - 200
13X-RAY DIFFRACTION1CC201 - 300201 - 300
14X-RAY DIFFRACTION1CC301 - 363301 - 363
15X-RAY DIFFRACTION1CC376 - 383376 - 383
16X-RAY DIFFRACTION1DD5 - 1005 - 100
17X-RAY DIFFRACTION1DD101 - 200101 - 200
18X-RAY DIFFRACTION1DD201 - 300201 - 300
19X-RAY DIFFRACTION1DD301 - 364301 - 364
20X-RAY DIFFRACTION1DD376 - 383376 - 383
21X-RAY DIFFRACTION1EE5 - 1005 - 100
22X-RAY DIFFRACTION1EE101 - 200101 - 200
23X-RAY DIFFRACTION1EE201 - 300201 - 300
24X-RAY DIFFRACTION1EE301 - 364301 - 364
25X-RAY DIFFRACTION1EE376 - 383376 - 383
26X-RAY DIFFRACTION1FF5 - 1005 - 100
27X-RAY DIFFRACTION1FF101 - 200101 - 200
28X-RAY DIFFRACTION1FF201 - 300201 - 300
29X-RAY DIFFRACTION1FF301 - 364301 - 364
30X-RAY DIFFRACTION1FF376 - 383376 - 383

+
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