[English] 日本語
Yorodumi
- PDB-5uou: High resolution structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoim... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uou
TitleHigh resolution structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Components2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) decarboxylase
KeywordsLYASE / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / Klebsiella pneumoniae subsp / Structural Genomics / Center For Structural Genomics Of Infectious Diseases (CSGID)
Function / homology
Function and homology information


2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase activity / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / urate catabolic process / purine nucleobase metabolic process / peroxisome
Similarity search - Function
2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, type 2 / UraD-like / Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase superfamily / OHCU decarboxylase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsChang, C. / Li, H. / Bearden, J. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: High resolution structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Authors: Chang, C. / Li, H. / Bearden, J. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) decarboxylase


Theoretical massNumber of molelcules
Total (without water)18,2911
Polymers18,2911
Non-polymers00
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.524, 61.524, 39.443
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) decarboxylase


Mass: 18291.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578) (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: KPN_01665 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: A6T925
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.06 Å3/Da / Density % sol: 40.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M Ammonium Acetate, 0.1 M HEPES, 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 23411 / % possible obs: 98.2 % / Redundancy: 7.7 % / Biso Wilson estimate: 12.51 Å2 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.019 / Rrim(I) all: 0.054 / Χ2: 0.887 / Net I/σ(I): 11.7 / Num. measured all: 180107
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.535.10.49710160.8450.2310.550.78386.1
1.53-1.5560.4230.9110.1790.460.78590.7
1.55-1.586.70.380.9430.1530.410.77695
1.58-1.627.40.3670.9430.1410.3940.78899.1
1.62-1.657.60.3120.9630.1190.3350.785100
1.65-1.6980.2840.9730.1070.3040.827100
1.69-1.738.10.220.9810.0820.2350.818100
1.73-1.788.10.1910.9830.0710.2040.809100
1.78-1.838.10.1490.9860.0560.1590.814100
1.83-1.898.10.1230.9910.0460.1310.823100
1.89-1.968.10.0980.9920.0360.1040.852100
1.96-2.048.10.0790.9910.0290.0840.864100
2.04-2.138.10.0620.9950.0230.0670.84100
2.13-2.248.20.0540.9960.020.0580.851100
2.24-2.388.10.0510.9960.0190.0550.886100
2.38-2.568.10.0510.9950.0190.0540.987100
2.56-2.828.10.0540.9960.020.0581.19100
2.82-3.238.10.0510.9960.0190.0551.253100
3.23-4.077.70.0370.9970.0150.040.86399.8
4.07-507.30.0390.9940.0160.0421.02793.4

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXdev_2650refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→27.514 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.51
RfactorNum. reflection% reflection
Rfree0.1965 2324 5.59 %
Rwork0.1626 --
obs0.1645 21679 89.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 53.44 Å2 / Biso mean: 18.1973 Å2 / Biso min: 6.94 Å2
Refinement stepCycle: final / Resolution: 1.5→27.514 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1155 0 0 214 1369
Biso mean---29.72 -
Num. residues----150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151316
X-RAY DIFFRACTIONf_angle_d1.4071790
X-RAY DIFFRACTIONf_chiral_restr0.088190
X-RAY DIFFRACTIONf_plane_restr0.009251
X-RAY DIFFRACTIONf_dihedral_angle_d18.863520
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.53060.2293830.19151206128948
1.5306-1.56390.1975820.17961572165460
1.5639-1.60020.24461210.18061755187670
1.6002-1.64030.2451190.18522001212077
1.6403-1.68460.23261540.18042197235186
1.6846-1.73420.24061580.17862391254993
1.7342-1.79010.24231590.17942533269299
1.7901-1.85410.23221180.166125962714100
1.8541-1.92830.21691420.163126172759100
1.9283-2.01610.19591820.155725042686100
2.0161-2.12230.17741400.152125952735100
2.1223-2.25520.20771240.142625822706100
2.2552-2.42920.20291720.158325522724100
2.4292-2.67350.20451420.167625972739100
2.6735-3.060.19951170.172826022719100
3.06-3.85350.17451180.152426162734100
3.8535-27.5190.16841930.16082365255894

+
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