[English] 日本語
Yorodumi
- PDB-9r45: Spitrobot-2 advances time-resolvedcryo-trapping crystallography t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9r45
TitleSpitrobot-2 advances time-resolvedcryo-trapping crystallography to under 25 ms: Xylose isomerase (apo state)
ComponentsXylose isomerase
KeywordsISOMERASE / Xylose isomerase / Spitrobot-2
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 / Xylose isomerase-like superfamily
Similarity search - Domain/homology
: / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsHatton, C.E. / Spiliopoulou, M. / Schulz, E.C. / Mehrabi, P.
Funding support Germany, European Union, 5items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)European Union
German Research Foundation (DFG)458246365 Germany
German Research Foundation (DFG)451079909 Germany
German Federal Ministry for Education and Research01KI2114 Germany
CitationJournal: Commun Chem / Year: 2025
Title: Spitrobot-2 advances time-resolved cryo-trapping crystallography to under 25 ms.
Authors: Spiliopoulou, M. / Hatton, C.E. / Kollewe, M. / Leimkohl, J.P. / Schikora, H. / Tellkamp, F. / Mehrabi, P. / Schulz, E.C.
History
DepositionMay 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3382
Polymers43,2831
Non-polymers551
Water3,981221
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)173,3538
Polymers173,1334
Non-polymers2204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area31130 Å2
ΔGint-134 kcal/mol
Surface area46020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.498, 93.723, 98.033
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-667-

HOH

-
Components

#1: Protein Xylose isomerase


Mass: 43283.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rubiginosus (bacteria) / Gene: xylA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P24300, xylose isomerase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.4
Details: 10 mM HEPEs pH 7.5 0.2 M Lithium Sulphate 25% Peg3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.788→67.745 Å / Num. obs: 20717 / % possible obs: 88.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 18.56 Å2 / CC1/2: 0.983 / Net I/σ(I): 5.9
Reflection shellResolution: 1.788→2.018 Å / Num. unique obs: 977 / CC1/2: 0.547 / % possible all: 50.9

-
Processing

Software
NameVersionClassification
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
PHENIX1.21.1_5286refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→67.74 Å / SU ML: 0.2343 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.191
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2444 1084 5.23 %
Rwork0.1957 19629 -
obs0.1983 20713 55.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.7 Å2
Refinement stepCycle: LAST / Resolution: 1.79→67.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 1 221 3252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00723120
X-RAY DIFFRACTIONf_angle_d0.87394226
X-RAY DIFFRACTIONf_chiral_restr0.0474436
X-RAY DIFFRACTIONf_plane_restr0.0093575
X-RAY DIFFRACTIONf_dihedral_angle_d15.82291151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.870.467880.3159125X-RAY DIFFRACTION2.87
1.87-1.970.3626200.2886430X-RAY DIFFRACTION9.77
1.97-2.090.3695790.26261294X-RAY DIFFRACTION29.52
2.09-2.220.3035910.25461966X-RAY DIFFRACTION53.37
2.26-2.480.27831510.24762843X-RAY DIFFRACTION65.03
2.48-2.840.28072220.21663893X-RAY DIFFRACTION87.55
2.84-3.580.22862510.18794454X-RAY DIFFRACTION99.51
3.58-67.740.21092620.16344624X-RAY DIFFRACTION99.69

+
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