[English] 日本語
Yorodumi
- PDB-8bln: Structure of RutB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bln
TitleStructure of RutB
ComponentsUreidoacrylate amidohydrolase RutB
KeywordsHYDROLASE
Function / homologyUreidoacrylate amidohydrolase RutB / ureidoacrylate amidohydrolase / uracil catabolic process / nitrogen utilization / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / Ureidoacrylate amidohydrolase RutB
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsRajendran, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Biochemistry / Year: 2023
Title: Structural and Functional Characterization of the Ureidoacrylate Amidohydrolase RutB from Escherichia coli .
Authors: Busch, M.R. / Rajendran, C. / Sterner, R.
History
DepositionNov 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details / _pdbx_initial_refinement_model.type
Revision 1.2Mar 27, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ureidoacrylate amidohydrolase RutB
B: Ureidoacrylate amidohydrolase RutB
C: Ureidoacrylate amidohydrolase RutB
D: Ureidoacrylate amidohydrolase RutB
E: Ureidoacrylate amidohydrolase RutB
F: Ureidoacrylate amidohydrolase RutB
G: Ureidoacrylate amidohydrolase RutB
H: Ureidoacrylate amidohydrolase RutB


Theoretical massNumber of molelcules
Total (without water)201,8298
Polymers201,8298
Non-polymers00
Water16,195899
1
A: Ureidoacrylate amidohydrolase RutB
H: Ureidoacrylate amidohydrolase RutB


Theoretical massNumber of molelcules
Total (without water)50,4572
Polymers50,4572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-18 kcal/mol
Surface area16370 Å2
MethodPISA
2
B: Ureidoacrylate amidohydrolase RutB
G: Ureidoacrylate amidohydrolase RutB


Theoretical massNumber of molelcules
Total (without water)50,4572
Polymers50,4572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-22 kcal/mol
Surface area16050 Å2
MethodPISA
3
C: Ureidoacrylate amidohydrolase RutB
F: Ureidoacrylate amidohydrolase RutB


Theoretical massNumber of molelcules
Total (without water)50,4572
Polymers50,4572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-20 kcal/mol
Surface area15760 Å2
MethodPISA
4
D: Ureidoacrylate amidohydrolase RutB
E: Ureidoacrylate amidohydrolase RutB


Theoretical massNumber of molelcules
Total (without water)50,4572
Polymers50,4572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-19 kcal/mol
Surface area15900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.115, 125.107, 123.268
Angle α, β, γ (deg.)90.000, 93.215, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

-
Components

#1: Protein
Ureidoacrylate amidohydrolase RutB


Mass: 25228.578 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rutB, EcDH1_2631, ECDH1ME8569_0965 / Production host: Escherichia coli (E. coli) / References: UniProt: C9QZ65, ureidoacrylate amidohydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 899 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→41.08 Å / Num. obs: 139409 / % possible obs: 97.77 % / Redundancy: 6.8 % / Biso Wilson estimate: 23.35 Å2 / CC1/2: 0.995 / Net I/σ(I): 7.25
Reflection shellResolution: 1.88→1.947 Å / Num. unique obs: 13587 / CC1/2: 0.584

-
Processing

Software
NameVersionClassification
PHENIX1.18rc2_3793refinement
PHENIX1.18rc2_3793refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WT model

Resolution: 1.88→41 Å / SU ML: 0.3402 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.7994
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2963 13754 5.01 %
Rwork0.2504 261050 -
obs0.2527 139409 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.5 Å2
Refinement stepCycle: LAST / Resolution: 1.88→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13654 0 0 899 14553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007314010
X-RAY DIFFRACTIONf_angle_d0.898719115
X-RAY DIFFRACTIONf_chiral_restr0.05322139
X-RAY DIFFRACTIONf_plane_restr0.00642498
X-RAY DIFFRACTIONf_dihedral_angle_d6.0521874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.90.41053990.37397592X-RAY DIFFRACTION85.28
1.9-1.920.37734520.34258544X-RAY DIFFRACTION95.83
1.92-1.940.38364610.3348693X-RAY DIFFRACTION96.3
1.94-1.970.36374560.32428731X-RAY DIFFRACTION97.37
1.97-20.36284510.31488601X-RAY DIFFRACTION96.09
2-2.020.36364630.3118769X-RAY DIFFRACTION97.55
2.02-2.050.34864620.31188684X-RAY DIFFRACTION97.15
2.05-2.080.36674600.30738703X-RAY DIFFRACTION96.54
2.08-2.110.35594510.29478691X-RAY DIFFRACTION98.2
2.11-2.150.3394590.29458736X-RAY DIFFRACTION96.27
2.15-2.190.34424620.28878750X-RAY DIFFRACTION98.58
2.19-2.230.3414560.28518743X-RAY DIFFRACTION96.63
2.23-2.270.34024590.28578701X-RAY DIFFRACTION98.34
2.27-2.320.33164640.28128784X-RAY DIFFRACTION96.95
2.32-2.370.33454590.27588707X-RAY DIFFRACTION98.24
2.37-2.420.33394630.26778762X-RAY DIFFRACTION96.55
2.42-2.480.3044620.26538700X-RAY DIFFRACTION98.91
2.48-2.550.34074610.27068828X-RAY DIFFRACTION97.46
2.55-2.620.34244650.26978817X-RAY DIFFRACTION98.19
2.62-2.710.29814630.26028769X-RAY DIFFRACTION98.28
2.71-2.80.33834550.26898716X-RAY DIFFRACTION97.18
2.81-2.920.30654640.26338748X-RAY DIFFRACTION97.61
2.92-3.050.33084650.25868827X-RAY DIFFRACTION98.41
3.05-3.210.30214650.2618858X-RAY DIFFRACTION98.62
3.21-3.410.28834650.24488781X-RAY DIFFRACTION98.07
3.41-3.680.27154600.22528768X-RAY DIFFRACTION98.12
3.68-4.040.24034660.21318766X-RAY DIFFRACTION97.91
4.04-4.630.20984540.1878637X-RAY DIFFRACTION96.55
4.63-5.830.24144660.18498852X-RAY DIFFRACTION98.34
5.83-410.21774660.18668792X-RAY DIFFRACTION98.35

+
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://pdbjlvh1.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