[English] 日本語
Yorodumi
- PDB-1ozb: Crystal Structure of SecB complexed with SecA C-terminus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ozb
TitleCrystal Structure of SecB complexed with SecA C-terminus
Components
  • Preprotein translocase secA subunit
  • Protein-export protein secB
KeywordsPROTEIN TRANSPORT / ZINC BINDING MOTIF / PROTEIN-PROTEIN COMPLEX
Function / homology
Function and homology information


ABC-type protein transporter activity / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / plasma membrane => GO:0005886 / protein targeting / protein tetramerization / unfolded protein binding / protein transport ...ABC-type protein transporter activity / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / plasma membrane => GO:0005886 / protein targeting / protein tetramerization / unfolded protein binding / protein transport / protein folding / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Bacterial protein export chaperone SecB / Preprotein translocase subunit SecB / Bacterial Protein-export protein SecB / SecB-like / SecB-like superfamily / SEC-C motif / SEC-C motif / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold ...Bacterial protein export chaperone SecB / Preprotein translocase subunit SecB / Bacterial Protein-export protein SecB / SecB-like / SecB-like superfamily / SEC-C motif / SEC-C motif / 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 / Roll / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
Protein translocase subunit SecA / Protein-export protein SecB
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhou, J. / Xu, Z.
CitationJournal: NAT.STRUCT.BIOL. / Year: 2003
Title: Structural determinants of SecB recognition by SecA in bacterial protein translocation
Authors: Zhou, J. / Xu, Z.
History
DepositionApr 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein-export protein secB
B: Protein-export protein secB
C: Protein-export protein secB
D: Protein-export protein secB
E: Protein-export protein secB
F: Protein-export protein secB
G: Protein-export protein secB
H: Protein-export protein secB
I: Preprotein translocase secA subunit
J: Preprotein translocase secA subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,37012
Polymers159,23910
Non-polymers1312
Water00
1
A: Protein-export protein secB
B: Protein-export protein secB
C: Protein-export protein secB
D: Protein-export protein secB
I: Preprotein translocase secA subunit
J: Preprotein translocase secA subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7858
Polymers82,6546
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Protein-export protein secB
F: Protein-export protein secB
G: Protein-export protein secB
H: Protein-export protein secB


Theoretical massNumber of molelcules
Total (without water)76,5854
Polymers76,5854
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.500, 114.500, 286.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein
Protein-export protein secB


Mass: 19146.301 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: SECB OR HI0743 / Plasmid details: T7 promoter / Plasmid: pSJ4-SecBHi / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P44853
#2: Protein/peptide Preprotein translocase secA subunit


Mass: 3034.530 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: SECA OR HI0909 / Plasmid details: GST fusion / Plasmid: pGEX-2T-SecAcHi / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P43803
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.7
Details: PEG 2000, magnesium sulfate, benzamidine hydrochloride, glycine , pH 9.7, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
117.4 mg/mlprotein1drop
224.5 %(w/v)PEG20001reservoir
3200 mM1reservoirMgSO4
4100 mMglycine1reservoirpH9.7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 12, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 47436 / Num. obs: 47436 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 66.6 Å2 / Rsym value: 0.056 / Net I/σ(I): 31.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 6 / Num. unique all: 4587 / Rsym value: 0.294 / % possible all: 98.1
Reflection
*PLUS
Num. measured all: 323553 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 98.1 % / Rmerge(I) obs: 0.294

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SecB coordinate

Resolution: 2.8→38.16 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 3771 8.1 %RANDOM
Rwork0.226 ---
obs0.226 46316 96.9 %-
all-46316 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.6258 Å2 / ksol: 0.326798 e/Å3
Displacement parametersBiso mean: 57.3 Å2
Baniso -1Baniso -2Baniso -3
1--6.1 Å20 Å20 Å2
2---6.1 Å20 Å2
3---12.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.8→38.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9142 0 2 0 9144
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.86
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 633 8.8 %
Rwork0.327 6533 -
obs--92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMMYZN.TOP
X-RAY DIFFRACTION3MYZN.PAR
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 50 Å / % reflection Rfree: 8 % / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

+
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://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