[English] 日本語
Yorodumi
- PDB-9rcq: 1,2-propanediol dehydratase with no ligand additives -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9rcq
Title1,2-propanediol dehydratase with no ligand additives
ComponentsGlycyl radical protein
KeywordsLYASE / glycyl radical enzyme / 1 / 2-propanediol
Function / homology
Function and homology information


lyase activity / cytosol
Similarity search - Function
: / Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Glycine radical domain / Glycine radical domain profile.
Similarity search - Domain/homology
Glycyl radical protein
Similarity search - Component
Biological speciesRaoultella planticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKalnins, G. / Estere, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: 1,2-propanediol dehydratase with no ligand additives
Authors: Kalnins, G. / Estere, M.
History
DepositionMay 29, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycyl radical protein
B: Glycyl radical protein
C: Glycyl radical protein
D: Glycyl radical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,5288
Polymers366,2804
Non-polymers2484
Water2,414134
1
A: Glycyl radical protein
B: Glycyl radical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,2644
Polymers183,1402
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-5 kcal/mol
Surface area51090 Å2
MethodPISA
2
C: Glycyl radical protein
D: Glycyl radical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,2644
Polymers183,1402
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-6 kcal/mol
Surface area50060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.890, 131.890, 457.930
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

-
Components

#1: Protein
Glycyl radical protein


Mass: 91569.922 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Raoultella planticola (bacteria) / Gene: I8Y23_000693 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AAN5KVK2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 3.14 Å3/Da / Density % sol: 60.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.55 M ammonium acetate, 4.5% PEG 4000, 0.1 M Tris-HCl

-
Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 10, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.6→76.32 Å / Num. obs: 143122 / % possible obs: 100 % / Redundancy: 20.5 % / Biso Wilson estimate: 57.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.07 / Rrim(I) all: 0.231 / Χ2: 1.01 / Net I/σ(I): 12.3
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 21.1 % / Rmerge(I) obs: 2.7 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 6989 / CC1/2: 0.546 / Rpim(I) all: 0.861 / Rrim(I) all: 2.834 / Χ2: 0.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.17.1_3660refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→76.32 Å / SU ML: 0.3715 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1656
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2379 6864 4.8 %
Rwork0.1888 136128 -
obs0.1912 142992 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.3 Å2
Refinement stepCycle: LAST / Resolution: 2.6→76.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25154 0 16 134 25304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008425884
X-RAY DIFFRACTIONf_angle_d1.100335089
X-RAY DIFFRACTIONf_chiral_restr0.05493763
X-RAY DIFFRACTIONf_plane_restr0.00684671
X-RAY DIFFRACTIONf_dihedral_angle_d14.4773551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.630.36521880.29374517X-RAY DIFFRACTION99.98
2.63-2.660.35762190.28394466X-RAY DIFFRACTION100
2.66-2.690.35032220.27884514X-RAY DIFFRACTION100
2.69-2.730.32761960.27234491X-RAY DIFFRACTION100
2.73-2.760.36892150.27534477X-RAY DIFFRACTION100
2.76-2.80.31322320.27114500X-RAY DIFFRACTION99.98
2.8-2.840.33562380.27114438X-RAY DIFFRACTION99.98
2.84-2.880.3472170.27064519X-RAY DIFFRACTION100
2.88-2.930.34792500.25724501X-RAY DIFFRACTION100
2.93-2.980.32352260.25354450X-RAY DIFFRACTION100
2.98-3.030.30182450.2524468X-RAY DIFFRACTION100
3.03-3.080.30542300.24674506X-RAY DIFFRACTION100
3.08-3.140.27372540.2334515X-RAY DIFFRACTION100
3.14-3.210.28171990.23314479X-RAY DIFFRACTION100
3.21-3.280.30582350.23914504X-RAY DIFFRACTION100
3.28-3.350.30372220.23874531X-RAY DIFFRACTION100
3.35-3.440.27742610.23074451X-RAY DIFFRACTION100
3.44-3.530.25622420.21294532X-RAY DIFFRACTION100
3.53-3.630.26212270.20124513X-RAY DIFFRACTION100
3.63-3.750.24632190.1964566X-RAY DIFFRACTION100
3.75-3.880.23992410.18344528X-RAY DIFFRACTION100
3.88-4.040.20092070.16634516X-RAY DIFFRACTION100
4.04-4.220.21722680.15614548X-RAY DIFFRACTION100
4.22-4.450.19182070.15094562X-RAY DIFFRACTION100
4.45-4.720.18932500.14394571X-RAY DIFFRACTION99.96
4.72-5.090.2082070.14424617X-RAY DIFFRACTION100
5.09-5.60.20952050.1654619X-RAY DIFFRACTION100
5.6-6.410.22342350.17874640X-RAY DIFFRACTION100
6.41-8.070.20742550.15884673X-RAY DIFFRACTION100
8.08-76.320.15312520.13564916X-RAY DIFFRACTION99.67

+
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