[English] 日本語
Yorodumi
- PDB-3dmd: Structures and Conformations in Solution of the Signal Recognitio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dmd
TitleStructures and Conformations in Solution of the Signal Recognition Particle Receptor from the archaeon Pyrococcus furiosus
ComponentsSignal recognition particle receptor
KeywordsTRANSPORT PROTEIN / SIGNAL RECOGNITION PARTICLE RECEPTOR / FTSY / SRP-GTPase / PROTEIN-TARGETING
Function / homology
Function and homology information


signal recognition particle binding / signal-recognition-particle GTPase / SRP-dependent cotranslational protein targeting to membrane / GTPase activity / GTP binding / ATP hydrolysis activity / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
SRP54, nucleotide-binding domain / Signal-recognition particle receptor FtsY / SRP/SRP receptor, N-terminal / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain ...SRP54, nucleotide-binding domain / Signal-recognition particle receptor FtsY / SRP/SRP receptor, N-terminal / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsEgea, P.F. / Tsuruta, H. / Napetschnig, J. / Walter, P. / Stroud, R.M.
CitationJournal: Plos One / Year: 2008
Title: Structures of the Signal Recognition Particle Receptor from the Archaeon Pyrococcus furiosus: Implications for the Targeting Step at the Membrane.
Authors: Egea, P.F. / Tsuruta, H. / de Leon, G.P. / Napetschnig, J. / Walter, P. / Stroud, R.M.
History
DepositionJun 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Signal recognition particle receptor
A: Signal recognition particle receptor
C: Signal recognition particle receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,83319
Polymers109,3203
Non-polymers1,51316
Water8,449469
1
B: Signal recognition particle receptor
hetero molecules

B: Signal recognition particle receptor
hetero molecules

A: Signal recognition particle receptor
C: Signal recognition particle receptor
hetero molecules

A: Signal recognition particle receptor
C: Signal recognition particle receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,66638
Polymers218,6396
Non-polymers3,02632
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation3_455x-1/2,y+1/2,z1
crystal symmetry operation4_454-x-1/2,y+1/2,-z-11
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area14610 Å2
ΔGint-327 kcal/mol
Surface area80250 Å2
MethodPISA
2
B: Signal recognition particle receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8205
Polymers36,4401
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Signal recognition particle receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9166
Polymers36,4401
Non-polymers4765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Signal recognition particle receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0968
Polymers36,4401
Non-polymers6577
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.956, 102.368, 101.766
Angle α, β, γ (deg.)90.00, 119.81, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Signal recognition particle receptor / Dpa


Mass: 36439.906 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM3638 / Gene: PF1766 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) rosetta2 / References: UniProt: Q8U051
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 3.1 Å3/Da / Density % sol: 60.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.9-1.2M Lithium Sulfate, 0.4-0.6M Ammonium Sulfate, 100 mM Na Citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 31, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.21→88.4 Å / Num. all: 65992 / Num. obs: 65992 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 8.9
Reflection shellResolution: 2.21→2.33 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 1.4 / Num. unique all: 9460 / Rsym value: 0.766 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
ELVESrefinement
MOSFLMin ELVESdata reduction
SCALAin ELVESdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DM9

3dm9


Resolution: 2.21→65.06 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2000 3.05 %3.1% OF RANDOMLY SELECTED REFLECTIONS
Rwork0.189 ---
obs0.191 65548 98.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.919 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 42 Å2
Baniso -1Baniso -2Baniso -3
1-2.2675 Å20 Å2-2.9906 Å2
2--0.5839 Å20 Å2
3----3.0836 Å2
Refinement stepCycle: LAST / Resolution: 2.21→65.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7399 0 86 469 7954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067576
X-RAY DIFFRACTIONf_angle_d0.93910181
X-RAY DIFFRACTIONf_dihedral_angle_d15.8652858
X-RAY DIFFRACTIONf_chiral_restr0.0641174
X-RAY DIFFRACTIONf_plane_restr0.0031295
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.21-2.26530.30781330.274228422892
2.2653-2.32650.30791390.255440996
2.3265-2.3950.30231390.2424442097
3.693-4.22730.17931460.14314650100
4.2273-5.32560.1861480.13574673100
5.3256-65.08560.20751470.1754468099

+
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