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- PDB-1yf5: Cyto-Epsl: The Cytoplasmic Domain Of Epsl, An Inner Membrane Comp... -

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Basic information

Entry
Database: PDB / ID: 1yf5
TitleCyto-Epsl: The Cytoplasmic Domain Of Epsl, An Inner Membrane Component Of The Type II Secretion System Of Vibrio Cholerae
ComponentsGeneral secretion pathway protein L
KeywordsTRANSPORT PROTEIN / Type II secretion / secretory protein
Function / homology
Function and homology information


Gram-negative-bacterium-type cell wall / protein secretion by the type II secretion system / type II protein secretion system complex / plasma membrane
Similarity search - Function
GspL cytoplasmic domain, C-terminal subdomain / Nucleotidyltransferase; domain 5 - #380 / 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 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Type II secretion system protein L
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsAbendroth, J. / Murphy, P. / Mushtaq, A. / Sandkvist, M. / Bagdasarian, M. / Hol, W.G.
Citation
Journal: 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. / Sandkvist, M. / Bagdasarian, M. / Hol, W.G.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: The Structure of the Cytoplasmic Domain of Epsl, an Inner Membrane Component of the Type II Secretio System of Vibrio Cholerae: An Unusual Member of the Actin-Like ATPase Superfamily
Authors: Abendroth, J. / Bagdasarian, M. / Sandkvist, M. / Hol, W.G.
History
DepositionDec 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: General secretion pathway protein L


Theoretical massNumber of molelcules
Total (without water)28,5291
Polymers28,5291
Non-polymers00
Water1629
1
L: General secretion pathway protein L

L: General secretion pathway protein L


Theoretical massNumber of molelcules
Total (without water)57,0582
Polymers57,0582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Unit cell
Length a, b, c (Å)61.006, 88.707, 55.371
Angle α, β, γ (deg.)90.00, 106.01, 90.00
Int Tables number5
Space group name H-MC121
Detailsthe second half of the dimer is generated by the crystallographic two-fold: -x+2, y, -z

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Components

#1: Protein General secretion pathway protein L / Cholera toxin secretion protein epsL


Mass: 28528.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: epsL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21gold(DE3) / References: UniProt: P45782
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 15% PEG 6000, 150mM calcium acetate, 100mM tris pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97951 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.74→20 Å / Num. all: 7122 / Num. obs: 7122 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 87.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.1
Reflection shellResolution: 2.74→2.8 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.37 / % possible all: 81

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1w97

1w97


Resolution: 2.75→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.919 / SU B: 42.646 / SU ML: 0.35 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26881 353 5 %RANDOM
Rwork0.21299 ---
all0.21553 7112 --
obs0.21553 6747 95.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.835 Å2
Baniso -1Baniso -2Baniso -3
1-3.83 Å20 Å29.68 Å2
2---0.23 Å20 Å2
3---1.73 Å2
Refinement stepCycle: LAST / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 0 9 1873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221912
X-RAY DIFFRACTIONr_angle_refined_deg1.0381.9672611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5295239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16325.11686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.65415322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.681510
X-RAY DIFFRACTIONr_chiral_restr0.0610.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021439
X-RAY DIFFRACTIONr_nbd_refined0.1910.2787
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21271
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.255
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2970.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.23
X-RAY DIFFRACTIONr_mcbond_it0.2651.51216
X-RAY DIFFRACTIONr_mcangle_it0.42821919
X-RAY DIFFRACTIONr_scbond_it0.4633794
X-RAY DIFFRACTIONr_scangle_it0.7494.5691
LS refinement shellResolution: 2.75→2.896 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.346 49 -
Rwork0.343 833 -
obs--83.68 %
Refinement TLS params.Method: refined / Origin x: 45.6585 Å / Origin y: -4.0897 Å / Origin z: 12.534 Å
111213212223313233
T-0.0929 Å2-0.0659 Å2-0.111 Å2-0.0095 Å2-0.1411 Å2---0.1815 Å2
L6.3612 °23.1532 °2-3.3137 °2-9.8419 °2-3.5918 °2--7.3842 °2
S0.6691 Å °-0.5171 Å °0.5673 Å °0.9107 Å °-0.5181 Å °0.652 Å °-0.1158 Å °-0.2308 Å °-0.151 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LA2 - 2396 - 243
2X-RAY DIFFRACTION1LB251 - 2591 - 9

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