[English] 日本語
Yorodumi
- PDB-6ulo: Structure of an N-terminally truncated uncharacterized protein fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ulo
TitleStructure of an N-terminally truncated uncharacterized protein from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Copenhageni (strain Fiocruz L1-130)
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologymembrane / Lipoprotein
Function and homology information
Biological speciesLeptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of an N-terminally truncated uncharacterized protein from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Copenhageni (strain Fiocruz L1-130)
Authors: Abendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionOct 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1484
Polymers76,0772
Non-polymers712
Water18,3931021
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0742
Polymers38,0381
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0742
Polymers38,0381
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.440, 56.650, 60.990
Angle α, β, γ (deg.)98.637, 106.327, 83.326
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein Uncharacterized protein


Mass: 38038.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni (strain Fiocruz L1-130) (bacteria)
Strain: Fiocruz L1-130 / Gene: LIC_10985 / Plasmid: LpinA.19565.a.B2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: Q72TN2
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1021 / 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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: Molecular Dimensions Morpheus screen, condition H5: 10% w/v PEG 20 000, 20% v/v PEG MME 550: 20mM of each amino acid: sodium l-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine: 100mM ...Details: Molecular Dimensions Morpheus screen, condition H5: 10% w/v PEG 20 000, 20% v/v PEG MME 550: 20mM of each amino acid: sodium l-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine: 100mM MOPS/HEPES-Na pH 7.5: LpinA.195645.a.B2.PW386228 at 23mg/ml. Cryo: direct: tray 310523 h5: puck PAS1-8. For phasing a crystal from the same tray, well C1 (10% w/v PEG 20 000, 20% v/v PEG MME 550: 30mM of each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate: 100mM MES/imidazole pH 6.5) was incubated for 20sec in a mixture of 10% 5M sodium iodide in ethylene glycol (500mM final NaI concentration) and 90% reservoir solution. Diffraction data were collected in-house.Tray 310523 c1: puck LOF7-9

-
Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 21-ID-F10.97872
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT21.5418
Detector
TypeIDDetectorDate
RAYONIX MX-3001CCDAug 15, 2019
RIGAKU SATURN 944+2CCDSep 20, 2019
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1C(111)SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978721
21.54181
ReflectionResolution: 1.3→50 Å / Num. obs: 155840 / % possible obs: 95.3 % / Redundancy: 3.927 % / Biso Wilson estimate: 19.615 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.041 / Χ2: 1.052 / Net I/σ(I): 19.58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.3-1.333.9530.5572.35111650.8350.64592.6
1.33-1.373.9510.4462.94109890.8860.51692.9
1.37-1.413.9470.3743.56106560.9180.43393.2
1.41-1.453.9440.2984.48105120.9440.34493.6
1.45-1.53.9460.2245.9101090.9670.25994.1
1.5-1.553.940.177.7498080.9780.19694.3
1.55-1.613.9290.1369.6495250.9860.15794.9
1.61-1.683.9320.1111.8392440.990.12895.2
1.68-1.753.9380.08714.6589150.9930.10195.4
1.75-1.843.9420.06818.7984840.9950.07895.9
1.84-1.943.9340.05223.5681740.9970.0696.4
1.94-2.063.9320.0429.8276940.9980.04796.6
2.06-2.23.9110.03236.0673310.9990.03797.1
2.2-2.373.9060.02839.9867880.9990.03397.3
2.37-2.63.8920.02643.3462740.9990.0397.8
2.6-2.913.860.02446.4957310.9990.02898.1
2.91-3.363.8680.0251.2350280.9990.02398.7
3.36-4.113.8810.01855.5142930.9990.0298.8
4.11-5.813.9070.01756.4933180.9990.01999.1
5.81-503.8160.01856.4218020.9990.02198.5

-
Processing

Software
NameVersionClassification
PHENIX1.17refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
ARP/wARPmodel building
Cootmodel building
PARROTphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→32.24 Å / SU ML: 0.1214 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 17.6941
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1722 1916 1.23 %0
Rwork0.1375 153900 --
obs0.138 155816 95.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.46 Å2
Refinement stepCycle: LAST / Resolution: 1.3→32.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4926 0 2 1021 5949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00935257
X-RAY DIFFRACTIONf_angle_d1.11227169
X-RAY DIFFRACTIONf_chiral_restr0.0849815
X-RAY DIFFRACTIONf_plane_restr0.0071914
X-RAY DIFFRACTIONf_dihedral_angle_d14.33642041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.24021340.215610632X-RAY DIFFRACTION92.48
1.33-1.370.22191340.19110707X-RAY DIFFRACTION92.9
1.37-1.410.1991250.175910768X-RAY DIFFRACTION93.21
1.41-1.450.21351320.157310882X-RAY DIFFRACTION93.78
1.45-1.510.20931270.143510757X-RAY DIFFRACTION94.1
1.51-1.570.17781220.131410934X-RAY DIFFRACTION94.4
1.57-1.640.17291310.128110929X-RAY DIFFRACTION95.06
1.64-1.720.15551520.1310964X-RAY DIFFRACTION95.42
1.72-1.830.17021520.128211041X-RAY DIFFRACTION95.92
1.83-1.970.18221550.135211131X-RAY DIFFRACTION96.4
1.97-2.170.17581340.128311198X-RAY DIFFRACTION97
2.17-2.490.15741370.133811214X-RAY DIFFRACTION97.53
2.49-3.130.17081490.140811325X-RAY DIFFRACTION98.25
3.13-32.240.15871320.130611418X-RAY DIFFRACTION99.01

+
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