[English] 日本語
Yorodumi
- PDB-1m6n: Crystal structure of the SecA translocation ATPase from Bacillus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m6n
TitleCrystal structure of the SecA translocation ATPase from Bacillus subtilis
ComponentsPreprotein translocase secA
KeywordsPROTEIN TRANSPORT / protein translocation / atpase / transmembrane transport / helicase family structure / mechanochemisty
Function / homology
Function and homology information


cell envelope Sec protein transport complex / protein-exporting ATPase activity / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / protein targeting / membrane raft / ATP binding / metal ion binding ...cell envelope Sec protein transport complex / protein-exporting ATPase activity / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / protein targeting / membrane raft / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #230 / Pre-protein croslinking domain of SecA / SecA, preprotein cross-linking domain / Helical scaffold and wing domains of SecA / Helical scaffold and wing domains of SecA / SecA P-loop domain / SEC-C motif / SEC-C motif / SecA, C-terminal helicase domain / Protein translocase subunit SecA ...Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #230 / Pre-protein croslinking domain of SecA / SecA, preprotein cross-linking domain / Helical scaffold and wing domains of SecA / Helical scaffold and wing domains of SecA / SecA P-loop domain / SEC-C motif / SEC-C motif / SecA, C-terminal helicase domain / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain / SecA motor DEAD / SecA conserved site / SecA, Wing/Scaffold superfamily / SecA, preprotein cross-linking domain superfamily / SecA preprotein cross-linking domain / SecA Wing and Scaffold domain / SecA DEAD-like domain / SecA family signature. / SecA family profile. / SecA DEAD-like domain / SecA preprotein cross-linking domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Protein translocase subunit SecA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.7 Å
AuthorsHunt, J.F. / Weinkauf, S. / Henry, L. / Fak, J.J. / McNicholas, P. / Oliver, D.B. / Deisenhofer, J.
Citation
Journal: Science / Year: 2002
Title: Nucleotide Control of Interdomain Interactions in the Conformational Reaction Cycle of SecA
Authors: Hunt, J.F. / Weinkauf, S. / Henry, L. / Fak, J.J. / McNicholas, P. / Oliver, D.B. / Deisenhofer, J.
#1: Journal: To be Published / Year: 2002
Title: Ping-pong cross-validation in real space: a method to increase the phasing power of a partial model without risk of phase bias
Authors: Hunt, J.F. / Deisenhofer, J.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Conformational stabilization and crystallization of the SecA translocation ATPase from Bacillus subtilis
Authors: Weinkauf, S. / Hunt, J.F. / Scheuring, J. / Henry, L. / Fak, J.J. / Oliver, D.B. / Deisenhofer, J.
History
DepositionJul 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Preprotein translocase secA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0668
Polymers91,3941
Non-polymers6727
Water81145
1
A: Preprotein translocase secA
hetero molecules

A: Preprotein translocase secA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,13216
Polymers182,7882
Non-polymers1,34514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-y+1,-x+1,-z+2/31
Buried area8580 Å2
ΔGint-261 kcal/mol
Surface area68480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)130.833, 130.833, 150.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Cell settingtrigonal
Space group name H-MP3112
DetailsThe other subunit in the physiological dimer is generated by 1-y, 1-x, 2/3-z (4_665)

-
Components

#1: Protein Preprotein translocase secA / secA


Mass: 91393.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: Div / Plasmid: pT7-Div / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P28366
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 4.06 Å3/Da / Density % sol: 69.73 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2 M ammonium sulfate, 30% glycerol, 1 mM DTT, 100 mM BES, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 299K
Crystal grow
*PLUS
Details: Weinkauf, S., (2001) Acta Crystallogr., Sect.D, 57, 559.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115-20 mg/mlprotein1drop
2300 mMammonium sulfate1drop
31 mMdithiothreitol1drop
420 mMBES1droppH7.0
546-52 %satammonium sulfate1reservoir
628-32 %(v/v)glycerol1reservoir
720-100 mMBES1reservoirpH7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.986 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Dec 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.986 Å / Relative weight: 1
ReflectionResolution: 2.7→45 Å / Num. all: 40576 / Num. obs: 40372 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 18.9
Reflection shellResolution: 2.7→2.75 Å / Mean I/σ(I) obs: 2.14 / Num. unique all: 2018 / % possible all: 0.973
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 50 Å / % possible obs: 99.6 % / Rmerge(I) obs: 0.078

-
Processing

Software
NameVersionClassification
DMmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 2.7→45.24 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2936891.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.301 1616 5 %RANDOM
Rwork0.22 ---
obs0.22 32620 80.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 91.5959 Å2 / ksol: 0.330937 e/Å3
Displacement parametersBiso mean: 98.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.54 Å22.11 Å20 Å2
2---6.54 Å20 Å2
3---13.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.7→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6402 0 35 45 6482
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it7.191.5
X-RAY DIFFRACTIONc_mcangle_it11.262
X-RAY DIFFRACTIONc_scbond_it40.712
X-RAY DIFFRACTIONc_scangle_it39.942.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.381 179 5 %
Rwork0.355 3413 -
obs--53.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHTOPH
X-RAY DIFFRACTION2PARTOP
X-RAY DIFFRACTION3PARATOPH
Refinement
*PLUS
Rfactor obs: 0.22 / Rfactor Rfree: 0.304 / Rfactor Rwork: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.74
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.67
LS refinement shell
*PLUS
Rfactor Rfree: 0.381 / Rfactor Rwork: 0.355

+
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