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- PDB-5c9e: SepL -

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Basic information

Entry
Database: PDB / ID: 5c9e
TitleSepL
ComponentsSepL
KeywordsMEMBRANE PROTEIN / secretion system component
Function / homologyType III secretion system effector delivery regulator TyeA-related / Hypersensitivity response secretion-like, HrpJ / HrpJ-like domain / outer membrane / : / secretion / BROMIDE ION / SepL
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.21 Å
AuthorsBurkinshaw, B.J. / Strynadka, N.C.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structural analysis of SepL, an enteropathogenic Escherichia coli type III secretion system gatekeeper protein
Authors: Burkinshaw, B.J. / Souza, S.A. / Strynadka, N.C.J.
History
DepositionJun 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SepL
B: SepL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3316
Polymers65,0112
Non-polymers3204
Water1629
1
A: SepL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6653
Polymers32,5061
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SepL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6653
Polymers32,5061
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-26 kcal/mol
Surface area24450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.320, 84.320, 238.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein SepL


Mass: 32505.549 Da / Num. of mol.: 2 / Fragment: UNP residues 70-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sepL / Production host: Escherichia coli (E. coli) / References: UniProt: O52149
#2: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.42 Å3/Da / Density % sol: 64.04 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 0.1M SPG buffer pH 6, 25% PEG 1500, 3M NaCl additive

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.92023 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92023 Å / Relative weight: 1
ReflectionResolution: 3.21→84.32 Å / Num. obs: 14926 / % possible obs: 100 % / Redundancy: 18.5 % / Biso Wilson estimate: 81.53 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.028 / Net I/σ(I): 23.1 / Num. measured all: 275631 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1 / Rejects: 0 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all
3.21-3.4319.20.8184.75020126210.960.191
9.08-84.3215.30.02977.71213479410.007

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Processing

Software
NameVersionClassification
Aimless0.3.5data scaling
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.15data extraction
xia2data reduction
PHASERphasing
RefinementResolution: 3.21→79.51 Å / Cor.coef. Fo:Fc: 0.9274 / Cor.coef. Fo:Fc free: 0.9121 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.439
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 748 5.03 %RANDOM
Rwork0.2105 ---
obs0.2127 14857 99.97 %-
Displacement parametersBiso max: 191.38 Å2 / Biso mean: 97.91 Å2 / Biso min: 28.12 Å2
Baniso -1Baniso -2Baniso -3
1-6.9192 Å20 Å20 Å2
2--6.9192 Å20 Å2
3----13.8383 Å2
Refine analyzeLuzzati coordinate error obs: 0.815 Å
Refinement stepCycle: final / Resolution: 3.21→79.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4270 0 4 9 4283
Biso mean--132.23 44.87 -
Num. residues----526
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1601SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes118HARMONIC2
X-RAY DIFFRACTIONt_gen_planes586HARMONIC5
X-RAY DIFFRACTIONt_it4338HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion578SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5311SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4338HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5843HARMONIC21.25
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion21.37
LS refinement shellResolution: 3.21→3.47 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3466 143 4.81 %
Rwork0.2455 2829 -
all0.2501 2972 -
obs--99.97 %
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)
11.25890.72540.26753.46531.29314.4976-0.1782-0.00230.0866-0.01330.3209-0.25040.3130.5376-0.1427-0.29750.0806-0.065-0.02050.0788-0.160643.181868.016791.4009
22.05680.91850.20572.5994-0.71114.1204-0.13050.0125-0.19420.19780.12160.1098-0.2935-0.23740.009-0.15160.03610.1201-0.1410.0311-0.230217.911359.286695.8771
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|80 - A|350 }A80 - 350
2X-RAY DIFFRACTION2{ B|80 - B|348 }B80 - 348

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