[English] 日本語
Yorodumi
- PDB-8gyr: Crystal structure of a variable region segment of Leptospira host... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gyr
TitleCrystal structure of a variable region segment of Leptospira host-interacting outer surface protein, LigA
Components
  • Leptospira Immunoglobulin-like protein
  • LigA
KeywordsCELL ADHESION / Leptospira / Leptospira immunoglobulin-like protein (Lig) / microbial surface components recognizing adhesive matrix molecule (MSCRAMM)
Function / homologyInvasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / IODIDE ION / : / PHOSPHATE ION / LigA
Function and homology information
Biological speciesLeptospira interrogans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsKumar, P. / Akif, M.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)EMR/2016/001183 India
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Crystal structure of a variable region segment of Leptospira host-interacting outer surface protein, LigA, reveals the orientation of Ig-like domains.
Authors: Kumar, P. / Vyas, P. / Faisal, S.M. / Chang, Y.F. / Akif, M.
History
DepositionSep 23, 2022Deposition site: PDBJ / Processing site: PDBE
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Leptospira Immunoglobulin-like protein
B: LigA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,89723
Polymers37,7782
Non-polymers1,11821
Water5,675315
1
A: Leptospira Immunoglobulin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,38012
Polymers18,8111
Non-polymers56911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LigA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,51711
Polymers18,9671
Non-polymers54910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.219, 63.905, 171.839
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Leptospira Immunoglobulin-like protein


Mass: 18811.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: C0J1Q2
#2: Protein LigA


Mass: 18967.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans (bacteria) / Gene: ligA / Production host: Escherichia coli (E. coli) / References: UniProt: C0J1Q2

-
Non-polymers , 8 types, 336 molecules

#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 23% PEG 3350, 260mM Potassium Iodide and 100mM Bis-Tris Propane

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.87→85.92 Å / Num. obs: 31943 / % possible obs: 98.8 % / Redundancy: 6.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.113 / Net I/σ(I): 9.1
Reflection shellResolution: 1.87→1.91 Å / Num. unique obs: 1705 / CC1/2: 0.759

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
pointlessdata scaling
BUCCANEERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MOG

2mog


Resolution: 1.87→85.92 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.906 / SU B: 7.551 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23411 1527 4.8 %RANDOM
Rwork0.20757 ---
obs0.20885 30215 98.35 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.308 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å2-0 Å2-0 Å2
2--0.62 Å2-0 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.87→85.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2645 0 41 315 3001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0182697
X-RAY DIFFRACTIONr_bond_other_d0.0010.022614
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.8723652
X-RAY DIFFRACTIONr_angle_other_deg1.022.8566061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0825363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36726.15478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31115477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.236152
X-RAY DIFFRACTIONr_chiral_restr0.0790.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022987
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02509
X-RAY DIFFRACTIONr_mcbond_it1.411.0541458
X-RAY DIFFRACTIONr_mcbond_other1.411.0531457
X-RAY DIFFRACTIONr_mcangle_it2.0311.5711819
X-RAY DIFFRACTIONr_mcangle_other2.0321.5721820
X-RAY DIFFRACTIONr_scbond_it2.6391.3191239
X-RAY DIFFRACTIONr_scbond_other2.5771.3211236
X-RAY DIFFRACTIONr_scangle_other3.6881.8591828
X-RAY DIFFRACTIONr_long_range_B_refined6.1914.5322973
X-RAY DIFFRACTIONr_long_range_B_other6.06914.1252918
LS refinement shellResolution: 1.87→1.917 Å
RfactorNum. reflection% reflection
Rfree0.329 100 -
Rwork0.304 1746 -
obs--78.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4054-0.390.21431.7949-2.02222.6858-0.02050.04290.04360.0679-0.0053-0.0363-0.16670.00090.02580.1061-0.0133-0.00440.00790.00560.0051-14.0343.523-19.376
20.32370.6483-0.72191.5559-1.76112.14960.0632-0.0670.02950.1652-0.1021-0.0218-0.17420.15890.03890.1602-0.00420.00720.0379-0.02030.0368-16.075-3.6669.313
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 210
2X-RAY DIFFRACTION2B2 - 202

+
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