[English] 日本語
Yorodumi
- PDB-2c04: GMPPCP complex of SRP GTPase Ffh NG Domain at ultra-high resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2c04
TitleGMPPCP complex of SRP GTPase Ffh NG Domain at ultra-high resolution
ComponentsSIGNAL RECOGNITION PARTICLE PROTEIN
KeywordsSIGNALING PROTEIN / GMPPNP / GTP-BINDING / RNA-BINDING / SRP / SRP54 / NUCLEOTIDE-BINDING / SIGNAL PROTEIN
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
Similarity search - Function
SRP54, nucleotide-binding domain / 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, nucleotide-binding domain / 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
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Signal recognition particle protein
Similarity search - Component
Biological speciesTHERMUS AQUATICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsRamirez, U.D. / Preininger, A.M. / Freymann, D.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Nucleotide-Binding Flexibility in Ultrahigh-Resolution Structures of the Srp Gtpase Ffh
Authors: Ramirez, U.D. / Focia, P.J. / Freymann, D.M.
History
DepositionAug 25, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Oct 16, 2019Group: Advisory / Data collection / Other
Category: pdbx_database_status / pdbx_validate_polymer_linkage / reflns_shell
Item: _pdbx_database_status.status_code_sf / _pdbx_validate_polymer_linkage.dist ..._pdbx_database_status.status_code_sf / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_1 / _pdbx_validate_polymer_linkage.label_alt_id_2 / _reflns_shell.Rmerge_I_obs
Revision 1.3Dec 13, 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 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_symmetry / _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_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
A: SIGNAL RECOGNITION PARTICLE PROTEIN
B: SIGNAL RECOGNITION PARTICLE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2666
Polymers65,1432
Non-polymers1,1234
Water10,539585
1
A: SIGNAL RECOGNITION PARTICLE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1734
Polymers32,5721
Non-polymers6013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SIGNAL RECOGNITION PARTICLE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0932
Polymers32,5721
Non-polymers5211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.006, 54.440, 98.831
Angle α, β, γ (deg.)90.00, 97.16, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.804508, 0.001286, -0.593941), (0.015166, 0.999716, -0.018378), (0.059375, -0.023792, -0.804299)
Vector: 92.1906)

-
Components

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


Mass: 32571.637 Da / Num. of mol.: 2 / Fragment: NG, RESIDUES 1-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS AQUATICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O07347
#2: 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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMANDATORY FOR EFFICIENT EXPORT OF EXTRA-CYTOPLASMIC PROTEINS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 45 %
Description: DATA WERE COLLECTED IN THREE OVERLAPPING RESOLUTION RANGES
Crystal growpH: 4.7
Details: 30% MPD, 0.1M NAACETATE, PH4.7, 20MM CACL2, 0.15M KOACETATE, 2MM MGCL2, 2MM GMPPCP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 26, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.15→19.6 Å / Num. obs: 192311 / % possible obs: 94.3 % / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.7
Reflection shellResolution: 1.15→1.18 Å / Redundancy: 3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.4 / % possible all: 90.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JPN

1jpn


Resolution: 1.15→19.61 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.58 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18 13065 7.1 %RANDOM
Rwork0.143 ---
obs0.146 169992 89.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å2-0.44 Å2
2--0.16 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.15→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4557 0 66 585 5208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228559
X-RAY DIFFRACTIONr_bond_other_d0.0040.028358
X-RAY DIFFRACTIONr_angle_refined_deg1.4872.03811608
X-RAY DIFFRACTIONr_angle_other_deg0.772319300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.52751109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20622.93372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.466151567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.87815107
X-RAY DIFFRACTIONr_chiral_restr0.0670.21312
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029613
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021718
X-RAY DIFFRACTIONr_nbd_refined0.2320.21168
X-RAY DIFFRACTIONr_nbd_other0.1760.26638
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22861
X-RAY DIFFRACTIONr_nbtor_other0.0820.24228
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2508
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0950.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0110.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.253
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.2204
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.263
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0350.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1561.55622
X-RAY DIFFRACTIONr_mcbond_other1.6571.52233
X-RAY DIFFRACTIONr_mcangle_it4.73928613
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.29933347
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it10.7054.52994
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: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 818 -
Rwork0.199 10713 -
obs--80.65 %

+
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