[English] 日本語
Yorodumi
- PDB-1qkk: Crystal structure of the receiver domain and linker region of Dct... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qkk
TitleCrystal structure of the receiver domain and linker region of DctD from Sinorhizobium meliloti
ComponentsC4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN
KeywordsTRANSCRIPTIONAL REGULATORY PROTEIN / RECEIVER DOMAIN / 2-COMPONENT SIGNAL TRANSDUCTION / SIGMA-54 DEPENDENT TRANSCRIPTIONAL ACTIVATOR / BACTERIAL ENHANCER BINDING PROTEIN / HIGH SOLVENT CONTENT CRYSTAL
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part 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 ...Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part 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 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / 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
C4-dicarboxylate transport transcriptional regulatory protein DctD
Similarity search - Component
Biological speciesSINORHIZOBIUM MELILOTI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsMeyer, M.G. / Park, S. / Zeringue, L. / Staley, M. / Mckinstry, M. / Kaufman, R.I. / Zhang, H. / Yan, D. / Yennawar, N. / Farber, G.K. / Nixon, B.T.
Citation
Journal: Faseb J. / Year: 2001
Title: A dimeric two-component receiver domain inhibits the sigma54-dependent ATPase in DctD.
Authors: Meyer, M.G. / Park, S. / Zeringue, L. / Staley, M. / McKinstry, M. / Kaufman, R.I. / Zhang, H. / Yan, D. / Yennawar, N. / Yennawar, H. / Farber, G.K. / Nixon, B.T.
#1: Journal: Science / Year: 1987
Title: Crystallographic R Factor Refinement by Molecular Dynamics
Authors: Brunger, A.T. / Kuriyan, J. / Karplus, M.
History
DepositionJul 23, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.4May 8, 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: C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)16,8211
Polymers16,8211
Non-polymers00
Water3,675204
1
A: C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN

A: C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)33,6432
Polymers33,6432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.651, 58.769, 167.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsTHE MOLECULE EXISTS AS A DIMER IN SOLUTION . THE DIMER ISCOMPRISED OF MONOMERS FROM DIFFERENT UNIT CELLS.DIMERIZATION SURFACES OCCUR AT THE FACES OF THE UNIT CELL"BOX".

-
Components

#1: Protein C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN / DCTD


Mass: 16821.260 Da / Num. of mol.: 1 / Fragment: RESIDUES 2 TO 143, RECEIVER DOMAIN
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN WAS EXPRESSED WITH THE C-TERMINAL HIS-TAG, KLAAALEHHHHHH. COORDINATES ARE SUBMITTED ONLY FOR THE MONOMER, WHICH COMPRISES THE COMPLETE ASYMMETRIC UNIT.
Source: (gene. exp.) SINORHIZOBIUM MELILOTI (bacteria) / Strain: N.A. 1021 / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / Variant (production host): B834 PLYSS / References: UniProt: P13632
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A: RESIDUES 144 TO 156 ARE A HIS TAG
Source detailsTHE PROTEIN IS FROM N.A. STRAIN=1021 REFERENCE: JIANG J., GU B., ALBRIGHT L.M., NIXON B.T., ...THE PROTEIN IS FROM N.A. STRAIN=1021 REFERENCE: JIANG J., GU B., ALBRIGHT L.M., NIXON B.T., CONSERVATION BETWEEN CODING AND REGULATORY ELEMENTS OF RHIZOBIUM MELILOTI AND RHIZOBIUM LEGUMINOSARUM DCT GENES, J. BACTERIOL. 171:5244-5253(1989). THE SWISSPROT ENTRY, P13632/DCTD_RHIME DESCRIBES THE SEQUENCE FROM N.A. STRAIN=JJ1C10 REFERENCE: WATSON R.J., ANALYSIS OF THE C4-DICARBOXYLATE TRANSPORT GENES OF RHIZOBIUM MELILOTI: NUCLEOTIDE SEQUENCE AND DEDUCED PRODUCTS OF DCTA, DCTB, AND DCTD, MOL. PLANT MICROBE INTERACT. 3:174-181(1990). THE TWO VARIANTS DIFFER AT THE FOLLOWING RESIDUES N.A. 1021 (THIS WORK) N.A. JJ1C10 (P13632) SEQ: 43 GLY GLU SEQ: 68 ARG GLY SEQ: 70 ILE VAL THE N-TERMINAL MET RESIDUE IS CLEAVED IN VIVO.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 71 %
Description: DATA WERE COLLECTED AT BEAMLINE 17-ID (OR 17-BM) IN THE FACILITIES OF THEINDUSTRIAL MACROMOLECULAR CRYSTALLOGRAPHY ASSOCIATION COLLABORATIVE ACCESS TEAM (IMCA-CAT) AT THE ADVANCED PHOTON ...Description: DATA WERE COLLECTED AT BEAMLINE 17-ID (OR 17-BM) IN THE FACILITIES OF THEINDUSTRIAL MACROMOLECULAR CRYSTALLOGRAPHY ASSOCIATION COLLABORATIVE ACCESS TEAM (IMCA-CAT) AT THE ADVANCED PHOTON SOURCE.THESE FACILITIES ARE SUPPORTED BY THE COMPANIES OF THE INDUSTRIAL MACROMOLECULAR CRYSTALLOGRAPHY ASSOCIATION THROUGH A CONTRACT WITH ILLINOIS INSTITUTE OF TECHNOLOGY (IIT), EXECUTED THROUGH THE IIT'S CENTER FOR SYNCHROTRON RADIATION RESEARCH AND INSTRUMENTATION.
Crystal growpH: 5.6
Details: 50 MM NA SUCCINATE PH 5.6, 70 MM AMMONIUM PHOSPHATE MONOBASIC, 1 MM DTT
Crystal grow
*PLUS
Temperature: 294 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-7 mg/mlprotein1drop
250 mMsuccinate1reservoir
375 mM1reservoirNH4H2PO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.98333, 0.98100, 0.98076
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 27, 1998 / Details: NO FOCUSSING MIRROR
RadiationMonochromator: CRYOGENICALLY COOLED SI (111) MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.983331
20.9811
30.980761
ReflectionResolution: 1.7→20 Å / Num. obs: 61207 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 20 Å2 / Rsym value: 0.062 / Net I/σ(I): 34
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.324 / % possible all: 100
Reflection
*PLUS
Num. obs: 32439 / % possible obs: 86.1 % / Rmerge(I) obs: 0.059

-
Processing

Software
NameVersionClassification
CNS0.9refinement
HKL-2000(DENZO)data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→19.42 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1822253.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2778 9.9 %RANDOM
Rwork0.218 ---
obs0.218 27943 86.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.1063 Å2 / ksol: 0.415432 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1--3.27 Å20 Å20 Å2
2--0.87 Å20 Å2
3---2.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-20 Å
Luzzati sigma a0.01 Å0.02 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1055 0 0 204 1259
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.941.5
X-RAY DIFFRACTIONc_mcangle_it1.492
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it2.752.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.226 324 10 %
Rwork0.213 2908 -
obs--60.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.231 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

+
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