[English] 日本語
Yorodumi
- PDB-3luf: Structure of probable two-component system response regulator/GGD... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3luf
TitleStructure of probable two-component system response regulator/GGDEF domain protein
ComponentsTwo-component system response regulator/GGDEF domain protein
KeywordsSIGNALING PROTEIN / structural genomics / ASA_2441 / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase / diguanylate cyclase activity / cell adhesion involved in single-species biofilm formation / phosphorelay signal transduction system / metal ion binding / plasma membrane
Similarity search - Function
: / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...: / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Reverse transcriptase/Diguanylate cyclase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAeromonas salmonicida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Structure of probable two-component system response regulator/GGDEF domain protein
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Two-component system response regulator/GGDEF domain protein
B: Two-component system response regulator/GGDEF domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0589
Polymers59,7262
Non-polymers3327
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-39 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.195, 53.699, 57.887
Angle α, β, γ (deg.)75.390, 80.990, 77.410
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Two-component system response regulator/GGDEF domain protein


Mass: 29863.020 Da / Num. of mol.: 2 / Fragment: sequence database residues 2-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas salmonicida (bacteria) / Strain: A449 / Gene: ASA_2441 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4SNL2
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5, 25% PEG 3350, 0.2M MgCl2, Vapor diffusion, Sitting drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.76→40 Å / Num. all: 44744 / Num. obs: 44744 / % possible obs: 97.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.063 / Rsym value: 0.068 / Net I/σ(I): 56.3
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 6.9 / Num. unique all: 2183 / Rsym value: 0.187 / % possible all: 95.4

-
Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXEmodel building
SHELXDphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.76→40 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.859 / SU B: 2.399 / SU ML: 0.079 / SU R Cruickshank DPI: 0.139 / SU Rfree: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2263 5.1 %RANDOM
Rwork0.187 ---
obs0.189 44744 97.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 53.49 Å2 / Biso mean: 18.852 Å2 / Biso min: 7.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.36 Å2-0.29 Å2
2--0.67 Å2-0.58 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.76→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4083 0 16 169 4268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224169
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9735665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5815533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80624.129201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18215777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4031538
X-RAY DIFFRACTIONr_chiral_restr0.1070.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213161
X-RAY DIFFRACTIONr_mcbond_it0.9411.52584
X-RAY DIFFRACTIONr_mcangle_it1.73624195
X-RAY DIFFRACTIONr_scbond_it2.88631585
X-RAY DIFFRACTIONr_scangle_it4.724.51470
LS refinement shellResolution: 1.762→1.807 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 167 -
Rwork0.236 2990 -
all-3157 -
obs--93.54 %

+
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