[English] 日本語
Yorodumi
- PDB-8thp: PorX phosphatase null mutant (T271V) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8thp
TitlePorX phosphatase null mutant (T271V)
ComponentsResponse regulator receiver protein
KeywordsSIGNALING PROTEIN / Type-IX secretion system / response regulator / alkaline phosphatase
Function / homology
Function and homology information


phosphorelay signal transduction system
Similarity search - Function
PglZ domain / PglZ domain / : / Alkaline-phosphatase-like, core domain superfamily / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily
Similarity search - Domain/homology
Response regulator receiver protein
Similarity search - Component
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSaran, A. / Zeytuni, N.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Pnas Nexus / Year: 2024
Title: Unveiling the molecular mechanisms of the type IX secretion system's response regulator: Structural and functional insights.
Authors: Saran, A. / Kim, H.M. / Manning, I. / Hancock, M.A. / Schmitz, C. / Madej, M. / Potempa, J. / Sola, M. / Trempe, J.F. / Zhu, Y. / Davey, M.E. / Zeytuni, N.
History
DepositionJul 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Response regulator receiver protein
B: Response regulator receiver protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,2937
Polymers121,0412
Non-polymers2525
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-77 kcal/mol
Surface area40010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.089, 96.978, 130.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Response regulator receiver protein


Mass: 60520.293 Da / Num. of mol.: 2 / Mutation: T271V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / NBRC 14942 / NCIMB 11054 / UW101) (bacteria)
Strain: ATCC 17061 / DSM 2064 / JCM 8514 / NBRC 14942 / NCIMB 11054 / UW101
Gene: Fjoh_2906 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A5FFU4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.14
Details: 0.16 M calcium acetate, 0.08 M sodium cacodylate pH 6.14, 14.4% polyethylene glycol 8K, 20% Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.953 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 34201 / % possible obs: 99.9 % / Redundancy: 5 % / CC1/2: 0.99 / CC star: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.047 / Rrim(I) all: 0.108 / Χ2: 1.415 / Net I/σ(I): 7.6 / Num. measured all: 169922
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.6-2.645.10.36716560.8650.9630.1790.4090.60699.8
2.64-2.695.10.35917030.8650.9630.1730.40.665100
2.69-2.7450.31416740.8850.9690.1540.3510.7399.8
2.74-2.84.70.27916840.9050.9750.140.3130.81699.9
2.8-2.8650.25416810.9180.9780.1240.2830.87299.8
2.86-2.935.40.24516890.9440.9850.1140.2710.976100
2.93-35.40.22316790.9540.9880.1040.2460.976100
3-3.085.40.19417080.9590.9890.090.2141.187100
3.08-3.175.30.17417020.970.9920.0810.1921.286100
3.17-3.285.30.15616930.9720.9930.0750.1741.406100
3.28-3.395.20.13716890.9820.9960.0650.1521.542100
3.39-3.535.10.12616980.9870.9970.060.141.807100
3.53-3.695.10.10816980.9890.9970.0520.121.982100
3.69-3.884.90.09717230.9870.9970.0480.1092.057100
3.88-4.134.80.08717000.9910.9980.0430.0972.09299.9
4.13-4.454.50.07217290.9920.9980.0380.0822.20699.9
4.45-4.8940.06117290.9940.9980.0340.072.06599.9
4.89-5.64.30.06417400.9940.9980.0330.0721.91299.5
5.6-7.054.80.06217570.9960.9990.030.0691.81299.2
7.05-504.80.03718690.99910.0170.0411.65599.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→45.95 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.848 / SU B: 19.614 / SU ML: 0.393 / Cross valid method: THROUGHOUT / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30458 1800 5.3 %RANDOM
Rwork0.24968 ---
obs0.25256 32346 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.536 Å2
Baniso -1Baniso -2Baniso -3
1-3.32 Å2-0 Å20 Å2
2---1.09 Å20 Å2
3----2.23 Å2
Refinement stepCycle: 1 / Resolution: 2.6→45.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8257 0 10 44 8311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0128443
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168144
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.64111395
X-RAY DIFFRACTIONr_angle_other_deg0.3621.57118843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3015998
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.569520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.146101607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.050.21254
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029450
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021842
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_it4.6815.0524009
X-RAY DIFFRACTIONr_mcbond_other4.6815.0524009
X-RAY DIFFRACTIONr_mcangle_it7.2379.0814999
X-RAY DIFFRACTIONr_mcangle_other7.2369.0815000
X-RAY DIFFRACTIONr_scbond_it4.295.3174434
X-RAY DIFFRACTIONr_scbond_other4.295.3174435
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8669.6726396
X-RAY DIFFRACTIONr_long_range_B_refined12.44861.2336682
X-RAY DIFFRACTIONr_long_range_B_other12.44861.2336683
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.604→2.671 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 120 -
Rwork0.355 2288 -
obs--96.86 %

+
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