[English] 日本語
Yorodumi
- PDB-1okk: HOMO-HETERODIMERIC COMPLEX OF THE SRP GTPASES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1okk
TitleHOMO-HETERODIMERIC COMPLEX OF THE SRP GTPASES
Components
  • CELL DIVISION PROTEIN FTSY
  • SIGNAL RECOGNITION PARTICLE PROTEIN
KeywordsCELL CYCLE / SIGNAL RECOGNITION-COMPLEX / SRP / FFH / FTSY / GTPASE / MEMBRANE TARGETING / SIGNAL SEQUENCE RECOGNITION
Function / homology
Function and homology information


signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / GTPase activity / GTP binding / ATP hydrolysis activity / plasma membrane / cytoplasm
Similarity search - Function
SRP54, nucleotide-binding domain / Signal-recognition particle receptor FtsY / Signal recognition particle protein / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle ...SRP54, nucleotide-binding domain / Signal-recognition particle receptor FtsY / Signal recognition particle protein / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / 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
N1-CARBOXYPIPERAZINE / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Signal recognition particle protein / Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesTHERMUS AQUATICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsFocia, P.J. / Freymann, D.M.
Citation
Journal: Science / Year: 2004
Title: Heterodimeric Gtpase Core of the Srp Targeting Complex
Authors: Focia, P.J. / Shepotinovskaya, I.V. / Seidler, J.A. / Freymann, D.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization of the Gmppcp Complex of the Ng Domains of T. Aquaticus Ffh and Ftsy
Authors: Shepotinovskaya, I.V. / Focia, P.J. / Freymann, D.M.
#2: Journal: Biochim.Biophys.Acta / Year: 2002
Title: Conformational Change of the N-Domain on Formation of the Complex between the Gtpase Domains of Thermus Aquaticus Ffh and Ftsy
Authors: Shepotinovskaya, I.V. / Freymann, D.M.
#3: Journal: Structure / Year: 2001
Title: The Conformation of Bound Gmppnp Suggests a Mechanism for Gating the Active Site of the Srp Gtpase
Authors: Padmanabhan, S. / Freymann, D.M.
History
DepositionJul 26, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SIGNAL RECOGNITION PARTICLE PROTEIN
D: CELL DIVISION PROTEIN FTSY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,92923
Polymers65,2732
Non-polymers2,65621
Water10,233568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.905, 98.905, 130.745
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsFOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350

-
Components

-
Protein , 2 types, 2 molecules AD

#1: Protein SIGNAL RECOGNITION PARTICLE PROTEIN / / FIFTY-FOUR HOMOLOG / FFH


Mass: 32300.371 Da / Num. of mol.: 1 / Fragment: NG DOMAIN, RESIDUES 0-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS AQUATICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O07347
#2: Protein CELL DIVISION PROTEIN FTSY /


Mass: 32972.230 Da / Num. of mol.: 1 / Fragment: NG DOMAIN, RESIDUES 2-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS AQUATICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P83749

-
Non-polymers , 6 types, 589 molecules

#3: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-BZP / N1-CARBOXYPIPERAZINE


Mass: 130.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10N2O2
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 568 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE UNIPROT ENTRY O07347 HAS ANNOTATION FOR THE INITIAL METHIONINE WHICH IN NOT INCLUDED IN THE SEQUENCE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 49.78 %
Crystal growpH: 6.7
Details: 1.91 M AMMONIUM SULFATE, 0.1 M BISTRIS PH 6.7, 0.1 M NACL, 4% PEG 400.
Crystal grow
*PLUS
Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDDetailsChemical formula
12000 nMprotein1
250 mMHEPES1pH7.5
32 mM1MgCl2
450 mM1NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 20, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→25 Å / Num. obs: 41332 / % possible obs: 99.9 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 33.4
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 16.2 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 25 Å

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NG1

1ng1


Resolution: 2.05→24.73 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.068 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE N-TERMINAL THREE RESIDUES OF FFH (A1 - A3) ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP. THE C- TERMINAL RESIDUE OF FFH (A 294) IS DISORDERED AND HAS BEEN OMITTED FROM THE MODEL. THE ...Details: THE N-TERMINAL THREE RESIDUES OF FFH (A1 - A3) ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP. THE C- TERMINAL RESIDUE OF FFH (A 294) IS DISORDERED AND HAS BEEN OMITTED FROM THE MODEL. THE FIRST 20 AMINO ACIDS OF FTSY (CHAIN D) ARE PROTEOLYTICALLY CLEAVED AND ARE NOT ASSOCIATED WITH THE COMPLEX OR SEEN IN THE CRYSTAL STRUCTURE. FTSY (CHAIN D) IS PROTEOLYTICALLY CLEAVED AT RESIDUE 90, IN THE LINKER BETWEEN THE N AND G DOMAINS. RESIDUES D 79 - D 96 OF THE LINKER REGION ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP. THE C-TERMINAL RESIDUE OF FTSY (D 304) IS NOT VISIBLE IN THE ELECTRON DENSITY MAP. ELECTRON DENSITY FOR FTSY LOOP D60 - D62 IS VERY POORLY DEFINED, AND THE CONFORMATION MAY BE INCORRECT. AN UNUSUAL PARTIAL RING OF ELECTRON DENSITY ENCIRCLES LYS D215 AND HAS BEEN MODELED AS TWO ETHYLENE GLYCOL MOLECULES, BUT SOME POSITIVE DIFFERENCE DENSITY REMAINS
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2046 5.1 %RANDOM
Rwork0.154 ---
obs0.156 38265 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---0.29 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.05→24.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4233 0 155 568 4956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214481
X-RAY DIFFRACTIONr_bond_other_d0.0020.024262
X-RAY DIFFRACTIONr_angle_refined_deg1.4542.0366057
X-RAY DIFFRACTIONr_angle_other_deg0.79539892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0865560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024843
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02831
X-RAY DIFFRACTIONr_nbd_refined0.1980.2983
X-RAY DIFFRACTIONr_nbd_other0.2360.25004
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.22753
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2458
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3150.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6421.52765
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25824421
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.16831716
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7434.51636
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.194 144
Rwork0.143 2862
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.475
LS refinement shell
*PLUS
Rfactor Rfree: 0.192 / Rfactor Rwork: 0.142

+
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