[English] 日本語
Yorodumi
- PDB-3p3q: Crystal Structure of MmoQ Response regulator from Methylococcus c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p3q
TitleCrystal Structure of MmoQ Response regulator from Methylococcus capsulatus str. Bath at the resolution 2.4A, Northeast Structural Genomics Consortium Target McR175M
ComponentsMmoQ
KeywordsTRANSCRIPTION / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


diguanylate cyclase / negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase activity / cell adhesion involved in single-species biofilm formation / phosphorelay signal transduction system / plasma membrane
Similarity search - Function
Metal-dependent hydrolase HDOD / HDOD domain / HD-related output (HDOD) domain profile. / Hypothetical protein af1432 / Hypothetical protein af1432 / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase ...Metal-dependent hydrolase HDOD / HDOD domain / HD-related output (HDOD) domain profile. / Hypothetical protein af1432 / Hypothetical protein af1432 / 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 / Reverse transcriptase/Diguanylate cyclase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMethylococcus capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKuzin, A.P. / Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Janjua, J. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, H. / Everett, J.K. ...Kuzin, A.P. / Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Janjua, J. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target McR175M
Authors: Kuzin, A.P. / Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Janjua, J. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / ...Authors: Kuzin, A.P. / Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Janjua, J. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionOct 5, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionNov 10, 2010ID: 3LJV
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MmoQ
B: MmoQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7796
Polymers62,4682
Non-polymers3114
Water1,51384
1
A: MmoQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4494
Polymers31,2341
Non-polymers2153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MmoQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3302
Polymers31,2341
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-77 kcal/mol
Surface area22610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.231, 76.156, 160.281
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsmonomer,33.14 kD,98.2%

-
Components

#1: Protein MmoQ / Response regulator


Mass: 31233.928 Da / Num. of mol.: 2 / Mutation: R49S, A242T, W293R, P300G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus (bacteria) / Gene: MCA1203, mmoQ, MMOQ; / Plasmid: PET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ MAGIC / References: UniProt: Q7WZ31
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.16 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 40031 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.2 / % possible all: 97.2

-
Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LJV

3ljv
PDB Unreleased entry


Resolution: 2.4→38.248 Å / SU ML: 0.33 / σ(F): 1.33 / Phase error: 24.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2553 1109 5.12 %
Rwork0.1938 --
obs0.197 21674 98.56 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.926 Å2 / ksol: 0.388 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.4044 Å2-0 Å2-0 Å2
2---1.3072 Å20 Å2
3----7.0971 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3776 0 16 84 3876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083842
X-RAY DIFFRACTIONf_angle_d1.055216
X-RAY DIFFRACTIONf_dihedral_angle_d16.4641402
X-RAY DIFFRACTIONf_chiral_restr0.066614
X-RAY DIFFRACTIONf_plane_restr0.005684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3991-2.50830.30391430.24372499X-RAY DIFFRACTION98
2.5083-2.64050.27111380.21372528X-RAY DIFFRACTION99
2.6405-2.80590.30871510.19952515X-RAY DIFFRACTION99
2.8059-3.02250.26521190.20762578X-RAY DIFFRACTION99
3.0225-3.32650.30091410.20222572X-RAY DIFFRACTION99
3.3265-3.80740.25871500.19472568X-RAY DIFFRACTION99
3.8074-4.79550.22321370.17022605X-RAY DIFFRACTION99
4.7955-38.25280.21671300.18672700X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -0.3762 Å / Origin y: -17.8726 Å / Origin z: -17.5589 Å
111213212223313233
T0.0765 Å2-0.0138 Å2-0.0016 Å2-0.093 Å20.0118 Å2--0.096 Å2
L0.5267 °20.2307 °20.0687 °2-0.1985 °20.0603 °2--0.5446 °2
S0.0093 Å °0.0343 Å °0.0613 Å °-0.0418 Å °0.0167 Å °0.053 Å °0.0149 Å °0.0319 Å °-0.0002 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