[English] 日本語
Yorodumi
- PDB-8zf3: Quorum Sensing Master Regulator SmcR of Photobacterium profundum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zf3
TitleQuorum Sensing Master Regulator SmcR of Photobacterium profundum
ComponentsHypothetical OpaR
KeywordsTRANSCRIPTION / Regulator
Function / homology: / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / transcription cis-regulatory region binding / DNA-binding transcription factor activity / Hypothetical OpaR
Function and homology information
Biological speciesPhotobacterium profundum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsBasu Choudhury, G. / Saha, A. / Raychaudhuri, S. / Datta, S.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR) India
CitationJournal: To Be Published
Title: Quorum Sensing Master Regulator SmcR of Photobacterium profundum
Authors: Basu Choudhury, G. / Saha, A. / Raychaudhuri, S. / Datta, S.
History
DepositionMay 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical OpaR
B: Hypothetical OpaR


Theoretical massNumber of molelcules
Total (without water)46,8132
Polymers46,8132
Non-polymers00
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-16 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.546, 45.901, 49.481
Angle α, β, γ (deg.)92.620, 91.050, 99.940
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein Hypothetical OpaR


Mass: 23406.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium profundum (bacteria) / Gene: SMCR, PBPRA3181 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q6LMJ0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 30% (v/v) MPD ,100 mM Sodium acetate/ Acetic acid pH 4.5, 25% (w/v) PEG 1500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Nov 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.78→25.82 Å / Num. obs: 37767 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 23.07 Å2 / CC1/2: 0.99 / Net I/σ(I): 20
Reflection shellResolution: 1.78→1.84 Å / Num. unique obs: 3808 / CC1/2: 0.871

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XXO

7xxo


Resolution: 1.78→22.58 Å / SU ML: 0.1851 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 26.6092
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2309 1687 4.78 %
Rwork0.19 33620 -
obs0.192 35307 93.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.24 Å2
Refinement stepCycle: LAST / Resolution: 1.78→22.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3110 0 0 344 3454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01233196
X-RAY DIFFRACTIONf_angle_d1.60174328
X-RAY DIFFRACTIONf_chiral_restr0.0505472
X-RAY DIFFRACTIONf_plane_restr0.0074568
X-RAY DIFFRACTIONf_dihedral_angle_d4.6196420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.830.26611240.25852330X-RAY DIFFRACTION77.02
1.83-1.890.27741250.24542472X-RAY DIFFRACTION83.48
1.89-1.960.28911390.24322635X-RAY DIFFRACTION88.6
1.96-2.040.29051260.22552780X-RAY DIFFRACTION92.46
2.04-2.130.28121440.21762835X-RAY DIFFRACTION94.15
2.13-2.240.25181490.20162877X-RAY DIFFRACTION96.22
2.24-2.380.25721350.19212906X-RAY DIFFRACTION96.14
2.38-2.570.22921440.19942902X-RAY DIFFRACTION97.29
2.57-2.820.27041480.20342938X-RAY DIFFRACTION98.12
2.82-3.230.23881620.19372963X-RAY DIFFRACTION99.21
3.23-4.070.17861490.16432984X-RAY DIFFRACTION99.59
4.07-22.580.20851420.1662998X-RAY DIFFRACTION99.49
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)
13.464270833591.061944235111.710343935062.666344596520.4533659476475.22261944179-0.1023054495790.2229312912330.120251986394-0.09388870973270.08834862841670.199232062882-0.360804774260.0664199321354-0.01751483166480.2042394556220.0111520205534-0.01960150802750.216815577996-0.01512084664640.1964137483513.7405247214-8.3562090621526.2927523112
21.210781576190.1026171699640.2109482774022.40899682313-0.7470935206054.05399701402-0.0183109995312-0.0177694990278-0.1421353100320.134269302087-0.00527578971398-0.04494836963550.216059155804-0.0468617175341-0.02328744327610.1549291703380.0339353947751-0.03533272230160.134713644068-0.01136973145580.17819947737127.7144438299-8.8564649540946.7636822781
35.362194690122.25403075811-2.604348246.54186633889-4.053505897975.01399297736-0.05314803078730.06075648143330.260192904646-0.01161219042770.2144609367770.2681416433260.0340213699815-0.202658262124-0.2103846424390.187778152820.0712704770665-0.05236928456140.22382491236-0.02175042439770.15368155207229.438055202221.556993246627.4623587247
42.56639874279-0.7368641793942.254935150383.43350018879-2.504895249017.55553099862-0.0482554819637-0.1667319328470.04545439118520.01442009135420.0215440900549-0.1052237056740.003356701628020.09256710900870.03327235618910.1414166289980.006417525258080.0216143491690.180860405165-0.02663784831920.12790316198233.350171275818.649163542428.0158418643
50.748359602401-0.258112770879-0.2281949563052.919668820470.402161259043.07552156201-0.00575099624056-0.08125418755630.008966198292320.1354635223850.0552742157419-0.2656344159410.03326356973120.385646229231-0.01180498486720.1328995503960.0145567067832-0.01210091511770.228863513521-0.01611095448570.13919333545535.57705850186.7258493717848.5768193428
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 12 through 83 )AA12 - 831 - 72
22chain 'A' and (resid 84 through 202 )AA84 - 20273 - 191
33chain 'B' and (resid 12 through 38 )BB12 - 381 - 27
44chain 'B' and (resid 39 through 83 )BB39 - 8328 - 72
55chain 'B' and (resid 84 through 201 )BB84 - 20173 - 190

+
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