[English] 日本語
Yorodumi
- PDB-7xp0: Crystal structure of PmiR from Pseudomonas aeruginosa -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xp0
TitleCrystal structure of PmiR from Pseudomonas aeruginosa
ComponentsProbable transcriptional regulator
KeywordsSIGNALING PROTEIN / PmiR / 2-methylcitrate cycle / bacterial virulence
Function / homology
Function and homology information


cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / metal ion binding
Similarity search - Function
FCD / GntR, C-terminal / FCD domain / Transcription regulator FadR/GntR, C-terminal / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Probable transcriptional regulator
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsZhang, Y.X. / Liang, H.H. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Adv / Year: 2022
Title: PmiR senses 2-methylisocitrate levels to regulate bacterial virulence in Pseudomonas aeruginosa.
Authors: Cui, G. / Zhang, Y. / Xu, X. / Liu, Y. / Li, Z. / Wu, M. / Liu, J. / Gan, J. / Liang, H.
History
DepositionMay 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 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: Probable transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3815
Polymers25,0271
Non-polymers3544
Water362
1
A: Probable transcriptional regulator
hetero molecules

A: Probable transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,76210
Polymers50,0552
Non-polymers7078
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-x-1,-y-1,z1
Buried area4150 Å2
ΔGint-171 kcal/mol
Surface area18630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.352, 74.352, 188.238
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

-
Components

#1: Protein Probable transcriptional regulator / PmiR


Mass: 25027.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0797 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I5E1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 54 % / Description: block
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: MES/Sodium hydroxide, Magnesium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 8283 / % possible obs: 98.6 % / Redundancy: 8.7 % / Biso Wilson estimate: 35.53 Å2 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.037 / Rrim(I) all: 0.121 / Χ2: 0.941 / Net I/σ(I): 15.1 / Num. measured all: 71992
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.694.60.4347500.660.1970.4820.96791.7
2.69-2.85.70.4087930.8240.1740.4460.90197.1
2.8-2.936.80.3348180.930.1330.3610.93599.6
2.93-3.087.20.278160.9680.1050.2910.91799.4
3.08-3.2880.2098150.9830.0740.2220.89699.5
3.28-3.539.50.1648270.9910.0530.1730.89299.8
3.53-3.8810.60.1258330.9920.0380.1310.94999.8
3.88-4.4410.90.1138440.9890.0340.1180.95899.6
4.44-5.5911.90.1178600.9930.0340.1221.09399.8
5.59-3010.70.1029270.9910.0330.1070.85399.6

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model generated by Alphafold2

Resolution: 2.61→29.38 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 25.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 353 4.92 %
Rwork0.1996 6816 -
obs0.2022 7169 84.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.47 Å2 / Biso mean: 49.669 Å2 / Biso min: 13.8 Å2
Refinement stepCycle: final / Resolution: 2.61→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1601 0 16 2 1619
Biso mean--72.29 46.27 -
Num. residues----200
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.61-2.980.3166720.24281455152756
2.99-3.760.27671410.2182590273198
3.76-29.380.221400.179627712911100
Refinement TLS params.Method: refined / Origin x: -32.8019 Å / Origin y: -26.1226 Å / Origin z: -23.2835 Å
111213212223313233
T0.1874 Å2-0.028 Å20.0802 Å2-0.3578 Å20.0632 Å2--0.2114 Å2
L2.2696 °20.092 °20.2337 °2-1.8619 °20.1463 °2--2.7702 °2
S0.0333 Å °0.5642 Å °0.3555 Å °-0.2477 Å °0.0605 Å °0.116 Å °-0.4655 Å °0.2118 Å °-0.0648 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA15 - 226
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allC1 - 3
4X-RAY DIFFRACTION1allD1 - 2

+
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