[English] 日本語
Yorodumi
- PDB-6qrt: X-ray radiation dose series on xylose isomerase - 1.38 MGy -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qrt
TitleX-ray radiation dose series on xylose isomerase - 1.38 MGy
ComponentsXylose isomerase
KeywordsMETAL BINDING PROTEIN / Isomerase
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. / : / 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
ISOPROPYL ALCOHOL / : / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsTaberman, H. / Bury, C.S. / van der Woerd, M.J. / Snell, E.H. / Garman, E.F.
Funding support Finland, 1items
OrganizationGrant numberCountry
Finnish Cultural Foundation Finland
CitationJournal: J.Synchrotron Radiat. / Year: 2019
Title: Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both.
Authors: Taberman, H. / Bury, C.S. / van der Woerd, M.J. / Snell, E.H. / Garman, E.F.
History
DepositionFeb 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,20520
Polymers43,1951
Non-polymers1,00919
Water9,476526
1
A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,81980
Polymers172,7814
Non-polymers4,03876
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area47210 Å2
ΔGint-89 kcal/mol
Surface area42640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.523, 97.518, 102.522
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-408-

EDO

21A-608-

HOH

31A-932-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Xylose isomerase


Mass: 43195.277 Da / Num. of mol.: 1 / Mutation: E186Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rubiginosus (bacteria) / Gene: xylA / Production host: Escherichia coli (E. coli) / References: UniProt: P24300, xylose isomerase

-
Non-polymers , 6 types, 545 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop
Details: 2-propanol, ethylene glycol, HEPES, magnesium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.954, 0.855
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9541
20.8551
ReflectionResolution: 1.17→38.7 Å / Num. obs: 154212 / % possible obs: 99.4 % / Redundancy: 3.5 % / Rrim(I) all: 0.087 / Net I/σ(I): 11.3
Reflection shellResolution: 1.17→1.19 Å / Rrim(I) all: 0.476

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3247: ???)refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QRR

6qrr


Resolution: 1.17→35.329 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 9.01
RfactorNum. reflection% reflection
Rfree0.1181 7706 5 %
obs0.1002 154200 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.17→35.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 58 526 3624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093755
X-RAY DIFFRACTIONf_angle_d1.1685132
X-RAY DIFFRACTIONf_dihedral_angle_d15.3071450
X-RAY DIFFRACTIONf_chiral_restr0.085511
X-RAY DIFFRACTIONf_plane_restr0.009716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.17-1.18330.20062450.19684662X-RAY DIFFRACTION96
1.1833-1.19720.17972460.18034741X-RAY DIFFRACTION98
1.1972-1.21180.17652530.1654843X-RAY DIFFRACTION99
1.2118-1.22720.16682590.14654889X-RAY DIFFRACTION100
1.2272-1.24330.17072590.13244864X-RAY DIFFRACTION100
1.2433-1.26030.12662540.12384845X-RAY DIFFRACTION100
1.2603-1.27840.13772560.12364881X-RAY DIFFRACTION100
1.2784-1.29740.13172560.11264883X-RAY DIFFRACTION100
1.2974-1.31770.13022580.10874871X-RAY DIFFRACTION100
1.3177-1.33930.13892540.10764897X-RAY DIFFRACTION100
1.3393-1.36240.12362600.1054901X-RAY DIFFRACTION100
1.3624-1.38720.12692560.09594871X-RAY DIFFRACTION100
1.3872-1.41390.11522540.08994864X-RAY DIFFRACTION100
1.4139-1.44270.1022580.0864886X-RAY DIFFRACTION100
1.4427-1.47410.10032590.07854899X-RAY DIFFRACTION100
1.4741-1.50840.0992570.07464916X-RAY DIFFRACTION100
1.5084-1.54610.10032550.07524852X-RAY DIFFRACTION100
1.5461-1.58790.10082590.0754918X-RAY DIFFRACTION100
1.5879-1.63460.09252570.07314899X-RAY DIFFRACTION100
1.6346-1.68740.08812610.07584934X-RAY DIFFRACTION100
1.6874-1.74770.09612550.0784886X-RAY DIFFRACTION100
1.7477-1.81770.09582590.08054927X-RAY DIFFRACTION100
1.8177-1.90040.09822570.0864896X-RAY DIFFRACTION100
1.9004-2.00060.09932600.08524951X-RAY DIFFRACTION100
2.0006-2.12590.09842590.08824920X-RAY DIFFRACTION100
2.1259-2.290.09522610.08744939X-RAY DIFFRACTION100
2.29-2.52040.10732590.08714934X-RAY DIFFRACTION100
2.5204-2.8850.11482610.09524983X-RAY DIFFRACTION100
2.885-3.63420.12422610.10274977X-RAY DIFFRACTION99
3.6342-35.34530.15762580.13114765X-RAY DIFFRACTION92

+
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