[English] 日本語
Yorodumi
- PDB-2bh1: X-ray structure of the general secretion pathway complex of the N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bh1
TitleX-ray structure of the general secretion pathway complex of the N- terminal domain of EpsE and the cytosolic domain of EpsL of Vibrio cholerae
Components
  • GENERAL SECRETION PATHWAY PROTEIN E,
  • GENERAL SECRETION PATHWAY PROTEIN L
KeywordsTRANSPORT PROTEIN / TYPE II SECRETION / VIBRIO CHOLERAE / EPS / GSP / TRANSMEMBRANE / TRANSPORT / ATP-BINDING
Function / homology
Function and homology information


protein-exporting ATPase activity / Gram-negative-bacterium-type cell wall / protein-secreting ATPase / protein secretion by the type II secretion system / type II protein secretion system complex / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Type II secretion system, protein E, N-terminal domain / GspL cytoplasmic domain, C-terminal subdomain / Nucleotidyltransferase; domain 5 - #380 / Type II secretion system protein GspE / Type II secretion system protein GspL / GspL, cytoplasmic actin-ATPase-like domain / GspL periplasmic domain / Type II secretion system (T2SS), protein L / GspL periplasmic domain / Type II secretion system protein GspE, N-terminal superfamily ...Type II secretion system, protein E, N-terminal domain / GspL cytoplasmic domain, C-terminal subdomain / Nucleotidyltransferase; domain 5 - #380 / Type II secretion system protein GspE / Type II secretion system protein GspL / GspL, cytoplasmic actin-ATPase-like domain / GspL periplasmic domain / Type II secretion system (T2SS), protein L / GspL periplasmic domain / Type II secretion system protein GspE, N-terminal superfamily / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein / GMP Synthetase; Chain A, domain 3 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Type II secretion system ATPase E / Type II secretion system protein L
Similarity search - Component
Biological speciesVIBRIO CHOLERAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAbendroth, J. / Murphy, P.M. / Mushtaq, A. / Bagdasarian, M. / Sandkvist, M. / Hol, W.G.J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The X-Ray Structure of the Type II Secretion System Complex Formed by the N-Terminal Domain of Epse and the Cytoplasmic Domain of Epsl of Vibrio Cholerae
Authors: Abendroth, J. / Murphy, P.M. / Mushtaq, A. / Bagdasarian, M. / Sandkvist, M. / Hol, W.G.J.
History
DepositionJan 6, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 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 / struct_conn / struct_ncs_dom_lim
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 / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GENERAL SECRETION PATHWAY PROTEIN L
B: GENERAL SECRETION PATHWAY PROTEIN L
X: GENERAL SECRETION PATHWAY PROTEIN E,
Y: GENERAL SECRETION PATHWAY PROTEIN E,
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3835
Polymers78,3434
Non-polymers401
Water3,189177
1
A: GENERAL SECRETION PATHWAY PROTEIN L
X: GENERAL SECRETION PATHWAY PROTEIN E,
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2123
Polymers39,1712
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: GENERAL SECRETION PATHWAY PROTEIN L
Y: GENERAL SECRETION PATHWAY PROTEIN E,


Theoretical massNumber of molelcules
Total (without water)39,1712
Polymers39,1712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.887, 89.325, 79.726
Angle α, β, γ (deg.)90.00, 91.16, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12X
22Y

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLYSLYSAA2 - 2392 - 239
21SERSERLYSLYSBB2 - 2392 - 239
12ILEILEGLNGLNXC14 - 8114 - 81
22ILEILEGLNGLNYD14 - 8114 - 81

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.1554, 0.8236, -0.5455), (0.8371, -0.1834, -0.5153), (-0.5244, -0.5367, -0.661)19.64, 1.084, 32.6
2given(-0.1285, 0.8661, -0.483), (0.7366, -0.2427, -0.6312), (-0.664, -0.4369, -0.6068)15.68, 8.174, 31.81
DetailsFOR THE HETERO_ASSEMBLY DESCRIBED BY REMARK 350

-
Components

#1: Protein GENERAL SECRETION PATHWAY PROTEIN L / CHOLERA TOXIN SECRETION PROTEIN / EPSL / GENERAL SECRETION PROTEIN EPSL


Mass: 27983.732 Da / Num. of mol.: 2 / Fragment: CYTOPLASMIC DOMAIN, RESIDUES 5-246
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VIBRIO CHOLERAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P45782
#2: Protein GENERAL SECRETION PATHWAY PROTEIN E, / TYPE II TRAFFIC WARDEN ATPASE / CHOLERA TOXIN SECRETION PROTEIN EPSE / GENERAL SECRETION PROTEIN EPSE


Mass: 11187.723 Da / Num. of mol.: 2 / Fragment: DOMAIN N1, RESIDUES 1-96
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VIBRIO CHOLERAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37093
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.3 Å3/Da / Density % sol: 45 %
Crystal growpH: 5.5
Details: 200MM CAOAC2, 100MM BISTRIS PH5.5, 25% PEG 3350, pH 5.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9999
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 27927 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.7
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W97

1w97


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 21.652 / SU ML: 0.253 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.412 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1381 4.9 %RANDOM
Rwork0.191 ---
obs0.194 26528 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.05 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å20 Å2-3.62 Å2
2---0.98 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4868 0 1 177 5046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224972
X-RAY DIFFRACTIONr_bond_other_d0.0010.024584
X-RAY DIFFRACTIONr_angle_refined_deg1.1371.9656768
X-RAY DIFFRACTIONr_angle_other_deg0.744310646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98524.783230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.32215852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8651528
X-RAY DIFFRACTIONr_chiral_restr0.0630.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025480
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02970
X-RAY DIFFRACTIONr_nbd_refined0.1830.2868
X-RAY DIFFRACTIONr_nbd_other0.1690.24601
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22316
X-RAY DIFFRACTIONr_nbtor_other0.0830.23150
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2181
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1030.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1320.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0640.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3071.53190
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.5224928
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.69632110
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.0994.51840
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
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3620loose positional0.555
2X1106loose positional0.575
1A3620loose thermal0.8910
2X1106loose thermal0.8810
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.346 94
Rwork0.293 1904
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.31640.76212.99554.20.97598.24270.3058-0.418-0.35520.3367-0.17950.49080.5661-0.9561-0.1263-0.1996-0.060.0197-0.01370.0213-0.0016-5.496-5.4528.799
26.2518-1.82986.02245.8496-1.84457.51350.05340.42970.2509-0.4572-0.16250.4323-0.145-0.11940.1091-0.04750.1314-0.04110.0985-0.0628-0.0136-10.878-0.881-14.672
38.9211-0.36770.55824.57931.27686.240.2250.81620.1818-0.156-0.1435-0.7701-0.47850.8602-0.0815-0.1498-0.01950.03350.0367-0.0021-0.033110.9363.66-4.856
42.9312-0.4529-0.27762.5267-0.08417.37910.2165-0.1009-0.39980.0790.15690.29271.1371-0.7634-0.3734-0.0035-0.104-0.0126-0.18760.0563-0.076611.046-6.61732.849
512.50050.07880.72521.9185-0.33947.25780.2685-0.6425-0.14460.4816-0.0917-0.4652-0.14581.2257-0.17680.056-0.0089-0.07720.0273-0.0431-0.017827.9760.13249.062
62.33680.85520.50112.7198-1.17954.6652-0.21340.10610.4912-0.26740.1781-0.3164-0.67060.33240.0353-0.1895-0.03960.1224-0.1848-0.0267-0.106822.88412.66728.01
711.4091-2.4272-1.47754.69070.67218.91020.0458-0.0209-0.6397-0.4082-0.2710.04150.2341-0.48310.2252-0.01650.0738-0.0696-0.1461-0.08690.03296.455-17.111-18.263
84.18612.77394.052317.10284.10828.75610.1315-0.60390.09371.0366-0.2581.15960.1344-0.7620.1265-0.01780.03310.1106-0.0414-0.0221-0.012215.77520.03350.807
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 61
2X-RAY DIFFRACTION1A115 - 141
3X-RAY DIFFRACTION1A217 - 239
4X-RAY DIFFRACTION2A62 - 114
5X-RAY DIFFRACTION3A142 - 216
6X-RAY DIFFRACTION4B2 - 61
7X-RAY DIFFRACTION4B115 - 141
8X-RAY DIFFRACTION4B217 - 239
9X-RAY DIFFRACTION5B62 - 114
10X-RAY DIFFRACTION6B142 - 216
11X-RAY DIFFRACTION7X14 - 81
12X-RAY DIFFRACTION8Y14 - 81

+
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