[English] 日本語
Yorodumi
- PDB-6ork: Crystal structure of Sel1 repeat protein from Oxalobacter formigenes -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ork
TitleCrystal structure of Sel1 repeat protein from Oxalobacter formigenes
ComponentsSel1 repeat protein
KeywordsHYDROLASE / Sel1 repeat / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homologySel1 repeat / Sel1-like repeat / Sel1-like repeats. / beta-lactamase activity / beta-lactamase / Tetratricopeptide-like helical domain superfamily / Sel1 repeat protein
Function and homology information
Biological speciesOxalobacter formigenes OXCC13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsChang, C. / Tesar, C. / Endres, M. / Babnigg, G. / Hassan, H. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Crystal structure of Sel1 repeat protein from Oxalobacter formigenes
Authors: Chang, C. / Tesar, C. / Endres, M. / Babnigg, G. / Hassan, H. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionApr 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sel1 repeat protein
B: Sel1 repeat protein
C: Sel1 repeat protein


Theoretical massNumber of molelcules
Total (without water)85,2013
Polymers85,2013
Non-polymers00
Water0
1
A: Sel1 repeat protein


Theoretical massNumber of molelcules
Total (without water)28,4001
Polymers28,4001
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sel1 repeat protein


Theoretical massNumber of molelcules
Total (without water)28,4001
Polymers28,4001
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sel1 repeat protein


Theoretical massNumber of molelcules
Total (without water)28,4001
Polymers28,4001
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.926, 103.368, 122.709
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Sel1 repeat protein


Mass: 28400.473 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oxalobacter formigenes OXCC13 (bacteria)
Gene: OFBG_00863 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3X9F9, beta-lactamase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 10 mM tri-sodium citrate, 33% PEG6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Aug 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 16196 / % possible obs: 98.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 48.91 Å2 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.039 / Rrim(I) all: 0.096 / Χ2: 0.861 / Net I/σ(I): 6.7 / Num. measured all: 93909
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.053.80.8936630.5980.4611.0120.96283.2
3.05-3.114.10.8397330.6850.4230.9460.93989.3
3.11-3.174.40.7147630.7640.3490.7990.90694.7
3.17-3.234.80.6227890.8470.2930.6910.94397.3
3.23-3.35.20.5347990.9050.2460.590.90799.1
3.3-3.385.50.4398130.9240.1980.4830.9499.8
3.38-3.465.70.3838100.9590.1710.420.9399.8
3.46-3.565.50.3018020.9660.1370.3320.91199.4
3.56-3.665.90.2358220.9750.1040.2570.861100
3.66-3.786.60.1947930.9880.0810.210.88799.6
3.78-3.916.60.1558330.9850.0650.1690.911100
3.91-4.076.70.1158070.9920.0480.1250.845100
4.07-4.266.50.0888180.9950.0370.0960.859100
4.26-4.486.40.0718340.9960.030.0770.79799.8
4.48-4.765.80.0658260.9940.0280.0710.78699.5
4.76-5.136.80.0688300.9950.0280.0740.787100
5.13-5.646.70.0658350.9940.0270.0710.78399.8
5.64-6.466.40.0588410.9950.0250.0630.809100
6.46-8.135.90.0438630.9940.0190.0470.8399.9
8.13-505.70.0349220.9980.0160.0370.81899.5

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 3→43.585 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.42
RfactorNum. reflection% reflection
Rfree0.2538 701 4.99 %
Rwork0.2091 --
obs0.2114 14231 81.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.73 Å2 / Biso mean: 43.6273 Å2 / Biso min: 10.42 Å2
Refinement stepCycle: final / Resolution: 3→43.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5751 0 0 0 5751
Num. residues----737
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9916-3.11140.4137640.33271170123436
3.1114-3.2530.3022820.29351645172751
3.253-3.42440.3758890.26012249233868
3.4244-3.63880.27831440.23742742288685
3.6388-3.91960.30651600.2233171333198
3.9196-4.31380.25441730.188732173390100
4.3138-4.93720.25471970.177531943391100
4.9372-6.21750.23091870.198832343421100
6.2175-43.58940.17951570.18633231338899

+
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