[English] 日本語
Yorodumi
- PDB-4f1r: Structure analysis of the global metabolic regulator Crc from Pse... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f1r
TitleStructure analysis of the global metabolic regulator Crc from Pseudomonas aeruginos
ComponentsCatabolite repression control protein
KeywordsTRANSCRIPTION REGULATOR / Catabolite Repression Control / post-transcription regulator
Function / homology
Function and homology information


double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / DNA repair / metal ion binding
Similarity search - Function
Exodeoxyribonuclease III-like / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Catabolite repression control protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsZhang, H. / Wei, Y. / Gao, Z.Q. / Dong, Y.H.
CitationJournal: Iubmb Life / Year: 2013
Title: Structure analysis of the global metabolic regulator Crc from Pseudomonas aeruginosa.
Authors: Wei, Y. / Zhang, H. / Gao, Z.Q. / Xu, J.H. / Liu, Q.S. / Dong, Y.H.
History
DepositionMay 7, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Catabolite repression control protein


Theoretical massNumber of molelcules
Total (without water)33,6151
Polymers33,6151
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.299, 74.299, 123.575
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Catabolite repression control protein


Mass: 33614.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: crc / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q51380
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.9M succinic acid pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2011
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 20524 / Num. obs: 20524 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 54.82
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 6.5 / Num. unique all: 1006 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WG8

1wg8


Resolution: 2.201→34.692 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 32.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 1035 5.11 %RANDOM
Rwork0.2022 ---
all0.2044 20524 --
obs0.2044 20273 98.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.285 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.6664 Å2-0 Å2-0 Å2
2--15.6664 Å20 Å2
3----31.3328 Å2
Refinement stepCycle: LAST / Resolution: 2.201→34.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2107 0 0 23 2130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072169
X-RAY DIFFRACTIONf_angle_d1.0362937
X-RAY DIFFRACTIONf_dihedral_angle_d16.606805
X-RAY DIFFRACTIONf_chiral_restr0.078299
X-RAY DIFFRACTIONf_plane_restr0.004389
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2011-2.31710.36551370.3254266396
2.3171-2.46220.37791670.2949266699
2.4622-2.65230.28671480.2507274199
2.6523-2.91910.31121430.2502273699
2.9191-3.34120.27281450.21762771100
3.3412-4.20830.22911520.18592815100
4.2083-34.69620.2071430.1713284696
Refinement TLS params.Method: refined / Origin x: -31.1686 Å / Origin y: 17.9614 Å / Origin z: 10.9351 Å
111213212223313233
T0.5384 Å2-0.0771 Å20.0288 Å2-0.4394 Å2-0.0022 Å2--0.4417 Å2
L1.8907 °20.1063 °2-0.5073 °2-2.1051 °2-0.4492 °2--3.9929 °2
S0.0063 Å °0.009 Å °0.0541 Å °-0.0502 Å °0.0729 Å °-0.0116 Å °-0.3324 Å °0.0076 Å °-0.0653 Å °
Refinement TLS groupSelection details: ALL

+
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