[English] 日本語
Yorodumi
- PDB-1rz3: Structure of a Possible Uridine Kinase from Bacillus stearothermo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rz3
TitleStructure of a Possible Uridine Kinase from Bacillus stearothermophilus
Componentshypothetical protein RBSTP0775
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Bacillus stearothermophilus / MCSG / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


kinase activity / ATP binding
Similarity search - Function
Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Rbstp0775 protein
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsCuff, M.E. / Joachimiak, A. / Wu, R.-Y. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of hypothetical protein RBSTP0775 from Bacillus stearothermophilus
Authors: Cuff, M.E. / Joachimiak, A. / Wu, R.-Y.
History
DepositionDec 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE AT THE TIME OF PROCESSING. THIS ...SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE AT THE TIME OF PROCESSING. THIS PROTEIN IS WIT DATABASE ID RBSTP0775.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hypothetical protein RBSTP0775
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5883
Polymers24,4891
Non-polymers992
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.010, 45.185, 107.023
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein hypothetical protein RBSTP0775


Mass: 24489.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: RBSTP0775 / Production host: Escherichia coli (E. coli) / References: UniProt: P84134
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2-propanol, MES pH6.0, calcium acetate, ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97896, 0.97910
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 16, 2003
RadiationMonochromator: sagitally focused Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978961
20.97911
ReflectionResolution: 1.9→34.45 Å / Num. all: 17505 / Num. obs: 17505 / % possible obs: 83.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.9 Å2 / Limit h max: 23 / Limit h min: 0 / Limit k max: 23 / Limit k min: 0 / Limit l max: 56 / Limit l min: 0 / Observed criterion F max: 1218158.9 / Observed criterion F min: 8.7
Reflection shellResolution: 1.9→1.99 Å / % possible all: 93.7

-
Processing

Software
NameVersionClassificationNB
CNS1.1refinement
d*TREKdata reduction
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→34.45 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 886 5.1 %random
Rwork0.203 ---
all0.203 17870 --
obs0.203 17505 98 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 67.5071 Å2 / ksol: 0.372362 e/Å3
Displacement parametersBiso max: 82.6 Å2 / Biso mean: 28.35 Å2 / Biso min: 11.42 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å20 Å20 Å2
2--3.44 Å20 Å2
3----2.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.11 Å
Luzzati d res high-1.9
Refinement stepCycle: LAST / Resolution: 1.9→34.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 5 217 1786
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg21.7
X-RAY DIFFRACTIONx_torsion_impr_deg0.67
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.9-1.990.292864.20.23219790.0322205206593.7
1.99-2.090.2471215.60.19120380.0222177215999.2
2.09-2.220.21044.70.19320880.022200219299.6
2.22-2.390.2641155.30.20220740.0252210218999
2.39-2.630.2191054.70.20821060.0212229221199.2
2.63-3.020.2481115.10.20420800.0242231219198.2
3.02-3.80.2431245.60.19120900.0222260221498
3.8-34.450.231205.30.20921640.0212376228496.1
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5ligand.paramligand.top

+
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