[English] 日本語
Yorodumi
- PDB-9lth: Crystal structure of transcriptional regulator (NrpR) from Strept... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9lth
TitleCrystal structure of transcriptional regulator (NrpR) from Streptococcus salivarius K12
ComponentsTranscriptional regulator
KeywordsTRANSCRIPTION / Streptococcus salivarius K12 / Transcriptional regulator
Function / homologyTranscription activator MutR, C-terminal / HTH-type transcriptional regulator Rgg, C-terminal domain / : / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / Transcriptional regulator
Function and homology information
Biological speciesStreptococcus salivarius K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsDo, H. / Nguyen, D.l. / Kumaraswami, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI182870-01A1 United States
CitationJournal: J.Bacteriol. / Year: 2025
Title: Environmental pH controls antimicrobial production by human probiotic Streptococcus salivarius.
Authors: Nguyen, D.L. / Saha, S. / Thacharodi, A. / Singh, B.B. / Mitra, S. / Do, H. / Kumaraswami, M.
History
DepositionFeb 6, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)34,0911
Polymers34,0911
Non-polymers00
Water19811
1
A: Transcriptional regulator

A: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)68,1832
Polymers68,1832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6090 Å2
ΔGint-36 kcal/mol
Surface area25500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.747, 128.260, 72.630
Angle α, β, γ (deg.)90.000, 100.616, 90.000
Int Tables number5
Space group name H-MI121

-
Components

#1: Protein Transcriptional regulator


Mass: 34091.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus salivarius K12 (bacteria)
Gene: RSSL_00023 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J7TTH6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 0.1 M Bis-Tris propane (pH 7.95), 0.7 M Sodium Citrate tribasic dihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9797 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.59→36.705 Å / Num. obs: 9474 / % possible obs: 97.4 % / Redundancy: 2.5 % / CC1/2: 0.99 / Net I/σ(I): 11.8
Reflection shellResolution: 2.59→2.71 Å / Num. unique obs: 2958 / CC1/2: 0.95

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→36.705 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.926 / SU B: 14.468 / SU ML: 0.303 / Cross valid method: FREE R-VALUE / ESU R Free: 0.364
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2659 458 4.834 %
Rwork0.1834 9016 -
all0.187 --
obs-9474 97.199 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 76.112 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.017 Å2
2--0.011 Å2-0 Å2
3---0.042 Å2
Refinement stepCycle: LAST / Resolution: 2.59→36.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2378 0 0 11 2389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132422
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162335
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.6313262
X-RAY DIFFRACTIONr_angle_other_deg1.2391.5765351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1275284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.2123.358137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89515463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7891512
X-RAY DIFFRACTIONr_chiral_restr0.0660.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022722
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02606
X-RAY DIFFRACTIONr_nbd_refined0.2040.2592
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.22201
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21230
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21098
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.257
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.190.242
X-RAY DIFFRACTIONr_nbd_other0.240.2127
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2480.211
X-RAY DIFFRACTIONr_mcbond_it6.7357.6891139
X-RAY DIFFRACTIONr_mcbond_other6.7067.6861138
X-RAY DIFFRACTIONr_mcangle_it9.57511.5331422
X-RAY DIFFRACTIONr_mcangle_other9.57611.5381423
X-RAY DIFFRACTIONr_scbond_it6.7378.4251279
X-RAY DIFFRACTIONr_scbond_other6.7348.4291280
X-RAY DIFFRACTIONr_scangle_it10.25812.3591839
X-RAY DIFFRACTIONr_scangle_other10.25512.3631840
X-RAY DIFFRACTIONr_lrange_it16.507146.95510040
X-RAY DIFFRACTIONr_lrange_other16.502146.92210038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.6570.399410.263675X-RAY DIFFRACTION97.019
2.657-2.730.359440.273618X-RAY DIFFRACTION98.806
2.73-2.8090.308250.282637X-RAY DIFFRACTION98.2196
2.809-2.8950.427360.268644X-RAY DIFFRACTION98.6938
2.895-2.990.265240.274581X-RAY DIFFRACTION98.6949
2.99-3.0950.313280.264598X-RAY DIFFRACTION98.4277
3.095-3.2110.37290.237561X-RAY DIFFRACTION98.4975
3.211-3.3420.364200.212539X-RAY DIFFRACTION98.0702
3.342-3.490.245270.184527X-RAY DIFFRACTION97.5352
3.49-3.660.324210.181475X-RAY DIFFRACTION98.2178
3.66-3.8570.287280.162486X-RAY DIFFRACTION99.2278
3.857-4.090.25250.163436X-RAY DIFFRACTION98.7152
4.09-4.3720.226230.134428X-RAY DIFFRACTION99.1209
4.372-4.720.215140.142388X-RAY DIFFRACTION98.5294
4.72-5.1680.205210.142363X-RAY DIFFRACTION98.7147
5.168-5.7730.265180.201337X-RAY DIFFRACTION99.4398
5.773-6.6570.324150.186276X-RAY DIFFRACTION97.3244
6.657-8.1310.161120.167244X-RAY DIFFRACTION97.3384
8.131-11.4080.20370.138130X-RAY DIFFRACTION66.5049
11.408-36.70500.2173X-RAY DIFFRACTION59.3496

+
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