[English] 日本語
Yorodumi
- PDB-5dy0: Crystal of AmtR from Corynebacterium glutamicum in complex with DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dy0
TitleCrystal of AmtR from Corynebacterium glutamicum in complex with DNA
Components
  • DNA
  • TetR family transcriptional regulator
KeywordsDNA BINDING PROTEIN / TetR family regulator / Nitrogen master regulator / PII / GlnK / GlnB / TFR
Function / homologyBacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / DNA binding / metal ion binding / DNA / DNA (> 10) / TetR family transcriptional regulator
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPalanca, C. / Rubio, V.
CitationJournal: Febs J. / Year: 2016
Title: Structure of AmtR, the global nitrogen regulator of Corynebacterium glutamicum, in free and DNA-bound forms.
Authors: Palanca, C. / Rubio, V.
History
DepositionSep 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TetR family transcriptional regulator
B: TetR family transcriptional regulator
C: TetR family transcriptional regulator
D: TetR family transcriptional regulator
E: DNA
F: DNA
G: DNA
H: DNA


Theoretical massNumber of molelcules
Total (without water)133,8498
Polymers133,8498
Non-polymers00
Water00
1
A: TetR family transcriptional regulator
B: TetR family transcriptional regulator
E: DNA
F: DNA


Theoretical massNumber of molelcules
Total (without water)66,9244
Polymers66,9244
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-54 kcal/mol
Surface area26430 Å2
MethodPISA
2
C: TetR family transcriptional regulator
D: TetR family transcriptional regulator
G: DNA
H: DNA


Theoretical massNumber of molelcules
Total (without water)66,9244
Polymers66,9244
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-50 kcal/mol
Surface area25210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.731, 137.423, 239.874
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

-
Components

#1: Protein
TetR family transcriptional regulator


Mass: 25477.975 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: ATCC 13969 / Gene: KIQ_008455 / Plasmid: pET-26 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A072Z681
#2: DNA chain
DNA


Mass: 7984.202 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Corynebacterium glutamicum (bacteria)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.26 Å3/Da / Density % sol: 80.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 1.2 M Trisodium Citrate, 0.1 M NaHepes pH 6.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→119.94 Å / Num. obs: 67304 / % possible obs: 99 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.029 / Net I/σ(I): 17.1 / Num. measured all: 295546 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3-3.074.60.6832.12090645250.7740.35899.8
14.07-119.943.40.02839.221556390.9990.01684.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
Aimless0.1.29data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DY1

5dy1


Resolution: 3→137.42 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.778 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.353 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22398 3348 5 %RANDOM
Rwork0.2058 ---
obs0.20677 62963 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 91.13 Å2
Baniso -1Baniso -2Baniso -3
1-7.98 Å20 Å20 Å2
2---1.92 Å20 Å2
3----6.06 Å2
Refinement stepCycle: LAST / Resolution: 3→137.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6590 2120 0 0 8710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0179093
X-RAY DIFFRACTIONr_bond_other_d0.0030.027627
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.7512821
X-RAY DIFFRACTIONr_angle_other_deg1.223317577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.425871
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.74422.9269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.104151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0581560
X-RAY DIFFRACTIONr_chiral_restr0.0780.21406
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218809
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021923
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.7449.093496
X-RAY DIFFRACTIONr_mcbond_other6.7439.093495
X-RAY DIFFRACTIONr_mcangle_it9.73813.6514363
X-RAY DIFFRACTIONr_mcangle_other9.73713.6524364
X-RAY DIFFRACTIONr_scbond_it8.4689.5825597
X-RAY DIFFRACTIONr_scbond_other8.4649.5835596
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.95714.2658458
X-RAY DIFFRACTIONr_long_range_B_refined16.56187.6438888
X-RAY DIFFRACTIONr_long_range_B_other16.56187.6438889
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 214 -
Rwork0.326 4142 -
obs--88.16 %

+
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