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- PDB-2bh1: X-ray structure of the general secretion pathway complex of the N... -

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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 / protein-secreting ATPase / Gram-negative-bacterium-type cell wall / 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 / : / GSPII protein E, N1E domain / 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 ...Type II secretion system, protein E, N-terminal domain / GspL cytoplasmic domain, C-terminal subdomain / Nucleotidyltransferase; domain 5 - #380 / : / GSPII protein E, N1E domain / 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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