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- PDB-4c47: Salmonella enterica trimeric lipoprotein SadB -

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Basic information

Entry
Database: PDB / ID: 4c47
TitleSalmonella enterica trimeric lipoprotein SadB
ComponentsINNER MEMBRANE LIPOPROTEIN
KeywordsCELL ADHESION / BACTERIAL ADHESION / MEMBRANE TRAFFICKING / MEMBRANE INSERTION / AUTOTRANSPORT / POLAR CORE RESIDUES
Function / homology
Function and homology information


Lipoprotein YajI-like / Domain of unknown function DUF3251 / Lipoprotein YajI-like superfamily / Protein of unknown function (DUF3251) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Inner membrane lipoprotein SadB
Similarity search - Component
Biological speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM STR. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.448 Å
AuthorsGrin, I. / Linke, D. / Hartmann, M.D.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: A Trimeric Lipoprotein Assists in Trimeric Autotransporter Biogenesis in Enterobacteria.
Authors: Grin, I. / Hartmann, M.D. / Sauer, G. / Hernandez Alvarez, B. / Schutz, M. / Madlung, J. / Macek, B. / Felipe-Lopez, A. / Hensel, M. / Lupas, A. / Linke, D.
History
DepositionSep 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Apr 2, 2014Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INNER MEMBRANE LIPOPROTEIN
B: INNER MEMBRANE LIPOPROTEIN
C: INNER MEMBRANE LIPOPROTEIN


Theoretical massNumber of molelcules
Total (without water)71,1973
Polymers71,1973
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11060 Å2
ΔGint-66 kcal/mol
Surface area29630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.450, 118.450, 159.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein INNER MEMBRANE LIPOPROTEIN / LIPOPROTEIN SADB


Mass: 23732.359 Da / Num. of mol.: 3 / Fragment: RESIDUES 23-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM STR. LT2 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8ZL65
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.1 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: SITTING DROP, TEMPERATURE 294K, RESERVOIR SOLUTION CONTAINING 0.2 M LITHIUM SULFATE, 0.1 M TRIS PH 8.5, 20% (W/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→39.5 Å / Num. obs: 30586 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.04 % / Biso Wilson estimate: 63.96 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.2
Reflection shellResolution: 2.45→2.6 Å / Redundancy: 3.93 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.86 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
SHELXphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.448→39.52 Å / SU ML: 0.34 / σ(F): 2.02 / Phase error: 28.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 1530 5 %
Rwork0.2043 --
obs0.2061 30586 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.448→39.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4499 0 0 28 4527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044567
X-RAY DIFFRACTIONf_angle_d0.7426186
X-RAY DIFFRACTIONf_dihedral_angle_d14.7051725
X-RAY DIFFRACTIONf_chiral_restr0.052734
X-RAY DIFFRACTIONf_plane_restr0.003788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4482-2.52730.31181380.29822620X-RAY DIFFRACTION98
2.5273-2.61760.29911400.28052654X-RAY DIFFRACTION100
2.6176-2.72230.3411380.26322618X-RAY DIFFRACTION100
2.7223-2.84620.29831390.26242650X-RAY DIFFRACTION100
2.8462-2.99620.31921410.25552673X-RAY DIFFRACTION100
2.9962-3.18390.31661380.25912624X-RAY DIFFRACTION100
3.1839-3.42960.28791390.23982639X-RAY DIFFRACTION100
3.4296-3.77450.23461400.21292663X-RAY DIFFRACTION100
3.7745-4.320.24341380.18852632X-RAY DIFFRACTION100
4.32-5.44050.20221400.16252645X-RAY DIFFRACTION100
5.4405-39.52470.18961390.17512638X-RAY DIFFRACTION99
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)
11.40720.42441.06584.48163.8134.0396-0.16720.5709-0.41940.6247-0.44750.8105-1.2541-0.14060.15231.3282-0.0533-0.02241.0843-0.43591.362812.791580.5787130.4142
21.6376-1.5298-1.85335.6062.34477.843-0.3557-0.30880.28730.25-0.23890.5713-0.4564-0.01660.28520.6149-0.0409-0.0590.6506-0.26541.202813.754768.6657110.085
32.36120.36580.54532.45551.60555.8119-0.3815-0.10340.575-0.344-0.06430.2749-0.36930.18510.41180.519-0.0425-0.01270.3949-0.09280.810514.281453.912985.3441
40.8364-0.3053-0.93283.16253.82754.40360.17150.1314-0.20790.0963-0.27070.18780.49720.02260.23250.8138-0.02580.02960.61750.00110.731212.170640.301561.5955
53.2741.7324-1.76586.85971.83764.33050.09770.14670.8524-0.243-0.0710.077-0.645-0.0741-0.1550.57350.1556-0.10050.29670.02750.77422.841444.379338.13
68.6876-3.4764-2.69142.60232.11413.1662-0.39190.2146-1.21440.28510.18210.79260.3467-0.27650.17240.51720.09050.01420.4398-0.01811.0689-6.865834.595844.6728
73.9811-0.96370.74015.7285-1.96336.1383-0.1811-0.3253-0.82810.7289-0.08830.08680.98380.47450.33710.96970.16590.01390.3607-0.01820.979117.779916.18750.3731
84.87710.3513-3.43510.0081-0.22392.4733-0.2746-0.15950.00121.29750.3271-0.2839-0.23611.0073-0.14991.18320.071-0.19850.5667-0.07021.112232.557253.822756.7807
96.93042.63042.2034.44445.61627.2304-0.0842-1.4970.79170.87820.12150.5956-1.08860.3590.30620.99810.2840.01091.0815-0.29471.154-10.540449.800161.5495
104.46530.7663-1.46182.9623-3.05453.2555-0.4325-0.56850.44710.2319-0.6175-0.8034-0.53120.6933-0.04962.38570.006-0.09471.17420.29650.955717.296815.163472.0641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 23:35) OR (CHAIN B AND RESSEQ 24:35) OR (CHAIN C AND RESSEQ 23:35)
2X-RAY DIFFRACTION2(CHAIN A AND RESSEQ 36:55) OR (CHAIN B AND RESSEQ 36:55) OR (CHAIN C AND RESSEQ 36:55)
3X-RAY DIFFRACTION3(CHAIN A AND RESSEQ 56:75) OR (CHAIN B AND RESSEQ 56:75) OR (CHAIN C AND RESSEQ 56:75)
4X-RAY DIFFRACTION4(CHAIN A AND RESSEQ 76:92) OR (CHAIN B AND RESSEQ 76:92) OR (CHAIN C AND RESSEQ 76:92)
5X-RAY DIFFRACTION5(CHAIN A AND RESSEQ 93:150) OR (CHAIN A AND RESSEQ 167:2139)
6X-RAY DIFFRACTION6(CHAIN B AND RESSEQ 93:150) OR (CHAIN B AND RESSEQ 167:213)
7X-RAY DIFFRACTION7(CHAIN C AND RESSEQ 93:150) OR (CHAIN C AND RESSEQ 167:215)
8X-RAY DIFFRACTION8(CHAIN A AND RESSEQ 151:166)
9X-RAY DIFFRACTION9(CHAIN B AND RESSEQ 151:166)
10X-RAY DIFFRACTION10(CHAIN C AND RESSEQ 151:166)

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