[English] 日本語
Yorodumi
- PDB-5i7g: Metal free Glucose Isomerase collected at room temperature using ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5i7g
TitleMetal free Glucose Isomerase collected at room temperature using the HC1b humidity controller
ComponentsXylose isomerase
KeywordsISOMERASE / Room temperature Metal-free
Function / homology
Function and homology information


xylose isomerase / xylose isomerase activity / D-xylose metabolic process / magnesium ion binding / identical protein binding / cytoplasm
Similarity search - Function
Xylose isomerase, actinobacteria / Xylose isomerase / Xylose isomerase family profile. / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsSandy, J.
CitationJournal: To Be Published
Title: Metal free Glucose Isomerase collected at room temperature using the HC1b humidity controller
Authors: Sandy, J.
History
DepositionFeb 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 2.0May 8, 2024Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Xylose isomerase


Theoretical massNumber of molelcules
Total (without water)43,2831
Polymers43,2831
Non-polymers00
Water5,314295
1
A: Xylose isomerase

A: Xylose isomerase

A: Xylose isomerase

A: Xylose isomerase


Theoretical massNumber of molelcules
Total (without water)173,1334
Polymers173,1334
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_557-x,y,-z+21
crystal symmetry operation4_557x,-y,-z+21
Buried area30120 Å2
ΔGint-110 kcal/mol
Surface area45600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.815, 99.698, 102.755
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

21A-652-

HOH

-
Components

#1: Protein Xylose isomerase


Mass: 43283.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10 mM Hepes pH 7.5, 1.6 M Ammonium Sulphate

-
Data collection

DiffractionMean temperature: 295 K
Ambient temp details: Collected using HC1b humidity controller
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 17, 2014
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.21→69.28 Å / Num. obs: 145645 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.121 / Net I/σ(I): 6
Reflection shellResolution: 1.21→1.24 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.68 / Mean I/σ(I) obs: 1 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→51.378 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.66
RfactorNum. reflection% reflection
Rfree0.1617 7173 4.94 %
Rwork0.1371 --
obs0.1383 145344 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.34 Å2
Refinement stepCycle: LAST / Resolution: 1.21→51.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2998 0 0 295 3293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163184
X-RAY DIFFRACTIONf_angle_d1.6064340
X-RAY DIFFRACTIONf_dihedral_angle_d17.1451187
X-RAY DIFFRACTIONf_chiral_restr0.178459
X-RAY DIFFRACTIONf_plane_restr0.01589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.22380.3842190.34434573X-RAY DIFFRACTION98
1.2238-1.23820.34822620.33584422X-RAY DIFFRACTION98
1.2382-1.25330.35022570.33174518X-RAY DIFFRACTION99
1.2533-1.26910.35452300.32384487X-RAY DIFFRACTION98
1.2691-1.28580.34382320.32074550X-RAY DIFFRACTION99
1.2858-1.30340.38022650.31374525X-RAY DIFFRACTION99
1.3034-1.32210.32612300.30324544X-RAY DIFFRACTION99
1.3221-1.34180.33192480.28614573X-RAY DIFFRACTION99
1.3418-1.36280.30692040.27084626X-RAY DIFFRACTION99
1.3628-1.38510.26852410.26384532X-RAY DIFFRACTION99
1.3851-1.4090.28752550.24984547X-RAY DIFFRACTION100
1.409-1.43460.27762470.23594577X-RAY DIFFRACTION100
1.4346-1.46220.27342430.21384592X-RAY DIFFRACTION100
1.4622-1.49210.21952540.20144605X-RAY DIFFRACTION100
1.4921-1.52450.21912310.18394585X-RAY DIFFRACTION100
1.5245-1.560.20672170.17064629X-RAY DIFFRACTION100
1.56-1.5990.19562320.14944599X-RAY DIFFRACTION100
1.599-1.64220.1822510.13654628X-RAY DIFFRACTION100
1.6422-1.69050.15332330.11954583X-RAY DIFFRACTION100
1.6905-1.74510.15252320.10924647X-RAY DIFFRACTION100
1.7451-1.80750.14652470.10294603X-RAY DIFFRACTION100
1.8075-1.87990.12711940.09854670X-RAY DIFFRACTION100
1.8799-1.96540.11912050.09074656X-RAY DIFFRACTION100
1.9654-2.0690.12242170.09164660X-RAY DIFFRACTION100
2.069-2.19870.11362830.09164627X-RAY DIFFRACTION100
2.1987-2.36840.11522550.09134626X-RAY DIFFRACTION100
2.3684-2.60680.11872380.09874690X-RAY DIFFRACTION100
2.6068-2.98390.1392590.11234668X-RAY DIFFRACTION100
2.9839-3.75930.12212850.11164700X-RAY DIFFRACTION100
3.7593-51.42390.12542070.1194929X-RAY DIFFRACTION100

+
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