[English] 日本語
Yorodumi
- PDB-2q5c: Crystal structure of NtrC family transcriptional regulator from C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q5c
TitleCrystal structure of NtrC family transcriptional regulator from Clostridium acetobutylicum
ComponentsNtrC family transcriptional regulator
KeywordsTRANSCRIPTION / structural genomics / NtrC family transcriptional regulator / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


phosphorelay response regulator activity / transcription factor binding / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP binding
Similarity search - Function
PrpR receptor domain-like / Signal transduction response regulator, propionate catabolism activator, N-terminal / Propionate catabolism activator / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain ...PrpR receptor domain-like / Signal transduction response regulator, propionate catabolism activator, N-terminal / Propionate catabolism activator / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / PAS fold / PAS fold / Response regulator / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Homeobox-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NtrC family transcriptional regulator (PAS and AAA domains)
Similarity search - Component
Biological speciesClostridium acetobutylicum ATCC 824 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.49 Å
AuthorsRamagopal, U.A. / Dickey, M. / Toro, R. / Iizuka, M. / Groshong, K. / Rodgers, L. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of NtrC family transcriptional regulator from Clostridium acetobutylicum.
Authors: Ramagopal, U.A. / Dickey, M. / Toro, R. / Iizuka, M. / Groshong, K. / Rodgers, L. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NtrC family transcriptional regulator
D: NtrC family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,29017
Polymers43,8652
Non-polymers1,42515
Water7,008389
1
A: NtrC family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5978
Polymers21,9321
Non-polymers6657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: NtrC family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6939
Polymers21,9321
Non-polymers7618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-138 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.950, 45.948, 58.284
Angle α, β, γ (deg.)72.94, 72.98, 82.07
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein NtrC family transcriptional regulator / PAS and AAA domains


Mass: 21932.260 Da / Num. of mol.: 2 / Fragment: Residues 2-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum ATCC 824 (bacteria)
Species: Clostridium acetobutylicum / Strain: DSM 792, JCM 1419, LMG 5710, VKM B-1787 / Gene: CA_C0459 / Plasmid: BS-pSGX4(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q97LU5
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 295 K / pH: 7.5
Details: 100mM Sodium Hepes pH 7.5, 2% PEG 400, 2M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 7.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 68459 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 18.4
Reflection shellResolution: 1.49→1.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.263 / % possible all: 87.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
SHELXC/D/Ephasing
RefinementMethod to determine structure: SAD / Resolution: 1.49→43.85 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.284 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 3455 5 %RANDOM
Rwork0.187 ---
obs0.188 68457 96.3 %-
all-68457 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20.8 Å20.18 Å2
2--0.55 Å2-0.29 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.49→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2920 0 79 389 3388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223208
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.432.0054344
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1535412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86925124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65115633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6431518
X-RAY DIFFRACTIONr_chiral_restr0.0990.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022264
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21529
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22250
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2316
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0511.52027
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75523241
X-RAY DIFFRACTIONr_scbond_it2.86331276
X-RAY DIFFRACTIONr_scangle_it4.4324.51102
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.49→1.53 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 228 -
Rwork0.219 4552 -
obs--90.07 %

+
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