[English] 日本語
Yorodumi
- PDB-6xia: REFINEMENT OF GLUCOSE ISOMERASE FROM STREPTOMYCES ALBUS AT 1.65 A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xia
TitleREFINEMENT OF GLUCOSE ISOMERASE FROM STREPTOMYCES ALBUS AT 1.65 ANGSTROMS WITH DATA FROM AN IMAGING PLATE
ComponentsD-XYLOSE ISOMERASE
KeywordsISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
Function / homology
Function and homology information


xylose isomerase / xylose isomerase activity / D-xylose metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
: / Xylose isomerase, actinobacteria / Xylose isomerase / Xylose isomerase family profile. / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces albus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsDauter, Z. / Terry, H. / Wilson, K.S.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1990
Title: Refinement of glucose isomerase from Streptomyces albus at 1.65 A with data from an imaging plate.
Authors: Dauter, Z. / Terry, H. / Witzel, H. / Wilson, K.S.
#1: Journal: FEBS Lett. / Year: 1989
Title: Crystallization and Preliminary Analysis of Glucose Isomerase from Streptomyces Albus
Authors: Dauter, Z. / Dauter, M. / Hemker, J. / Witzel, H. / Wilson, K.S.
History
DepositionSep 13, 1990Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-XYLOSE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)43,1311
Polymers43,1311
Non-polymers00
Water8,179454
1
A: D-XYLOSE ISOMERASE

A: D-XYLOSE ISOMERASE

A: D-XYLOSE ISOMERASE

A: D-XYLOSE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)172,5244
Polymers172,5244
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area30730 Å2
ΔGint-97 kcal/mol
Surface area46220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.900, 99.700, 102.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: RESIDUE 186 IS A CIS PROLINE.
2: ATOMS WITH AN OCCUPANCY OF 0.0 WERE NOT LOCATED IN THE ELECTRON DENSITY MAPS.
Components on special symmetry positions
IDModelComponents
11A-548-

HOH

21A-797-

HOH

-
Components

#1: Protein D-XYLOSE ISOMERASE


Mass: 43131.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albus (bacteria) / References: UniProt: P24299, xylose isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.92 %
Crystal grow
*PLUS
Temperature: 277 K / pH: 7.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlenzyme11
20.005 MHEPES11
31 Mammonium sulphate11

-
Data collection

Reflection
*PLUS
Highest resolution: 1.65 Å / Num. obs: 54575 / % possible obs: 94.6 % / Observed criterion σ(I): 3 / Num. measured all: 224189 / Rmerge(I) obs: 0.126 / Biso Wilson estimate: 14.3 Å2
Reflection shell
*PLUS
Highest resolution: 0.165 Å / Rmerge(I) obs: 0.126

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.65→8 Å
Details: ATOMS WITH AN OCCUPANCY OF 0.0 WERE NOT LOCATED IN THE ELECTRON DENSITY MAPS.
RfactorNum. reflection
obs0.141 54385
Refinement stepCycle: LAST / Resolution: 1.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3045 0 0 454 3499
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.1660.2
X-RAY DIFFRACTIONp_singtor_nbd0.1810.5
X-RAY DIFFRACTIONp_multtor_nbd0.2770.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1980.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.15
X-RAY DIFFRACTIONp_staggered_tor14.915
X-RAY DIFFRACTIONp_orthonormal_tor32.920
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 8 Å / Rfactor obs: 0.141
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20 Å2
Refine LS restraints
*PLUS
Type: p_dihedral_angle_d / Dev ideal target: 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