[English] 日本語
Yorodumi
- PDB-4u09: Structure of Leptospira interrogans LRR protein LIC12759 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4u09
TitleStructure of Leptospira interrogans LRR protein LIC12759
ComponentsLIC12759
KeywordsUNKNOWN FUNCTION / LRR PROTEIN / PATHOGEN / VIRULENCE FACTOR
Function / homology
Function and homology information


Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Cytoplasmic membrane protein
Similarity search - Component
Biological speciesLeptospira interrogans serovar Copenhageni str. Fiocruz L1-130 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsShepard, W. / Saul, F.A. / Haouz, A. / Picardeau, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural characterization of a novel subfamily of leucine-rich repeat proteins from the human pathogen Leptospira interrogans.
Authors: Miras, I. / Saul, F. / Nowakowski, M. / Weber, P. / Haouz, A. / Shepard, W. / Picardeau, M.
History
DepositionJul 11, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LIC12759
B: LIC12759
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,58417
Polymers92,2622
Non-polymers1,32215
Water10,971609
1
A: LIC12759
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7908
Polymers46,1311
Non-polymers6597
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LIC12759
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7949
Polymers46,1311
Non-polymers6638
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.166, 104.796, 116.597
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein LIC12759 / LIC12759


Mass: 46131.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 (bacteria)
Gene: LIC_12759 / Plasmid: PDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PLYSS / References: UniProt: Q72NS0

-
Non-polymers , 6 types, 624 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, 125 mM zinc acetate, 200 mM magnesium chloride, 100 mM MES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.28199 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2011
RadiationMonochromator: CHANNEL CUT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28199 Å / Relative weight: 1
ReflectionResolution: 1.95→47.79 Å / Num. obs: 67851 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 33.52 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 13.6
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 11 % / Rmerge(I) obs: 0.974 / Mean I/σ(I) obs: 2.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→47.79 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.8992 / SU R Cruickshank DPI: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.16 / SU Rfree Blow DPI: 0.136 / SU Rfree Cruickshank DPI: 0.134
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 984 1.45 %RANDOM
Rwork0.1869 ---
obs0.1873 67774 99.99 %-
Displacement parametersBiso mean: 43.7 Å2
Baniso -1Baniso -2Baniso -3
1--22.4237 Å20 Å20 Å2
2--9.15 Å20 Å2
3---13.2737 Å2
Refine analyzeLuzzati coordinate error obs: 0.246 Å
Refinement stepCycle: 1 / Resolution: 1.95→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6379 0 58 609 7046
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016503HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.158774HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2506SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes237HARMONIC2
X-RAY DIFFRACTIONt_gen_planes838HARMONIC5
X-RAY DIFFRACTIONt_it6503HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion18.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion841SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7791SEMIHARMONIC4
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 65 1.32 %
Rwork0.2518 4854 -
all0.2521 4919 -
obs--99.99 %

+
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