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- PDB-6qvp: Crystal structure of the peptidoglycan-binding domain of SiiA fro... -

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Basic information

Entry
Database: PDB / ID: 6qvp
TitleCrystal structure of the peptidoglycan-binding domain of SiiA from Salmonella enterica
ComponentsInner membrane protein
KeywordsMEMBRANE PROTEIN / OmpA-like domain / Peptidoglycan binding / periplasmic / Salmonella / T1SS
Function / homologymembrane / PHOSPHATE ION / Membrane protein
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsKirchweger, P. / Muller, Y.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationMU 1477/9-2 Germany
CitationJournal: Mol.Microbiol. / Year: 2019
Title: Structural and functional characterization of SiiA, an auxiliary protein from the SPI4-encoded type 1 secretion system from Salmonella enterica.
Authors: Kirchweger, P. / Weiler, S. / Egerer-Sieber, C. / Blasl, A.T. / Hoffmann, S. / Schmidt, C. / Sander, N. / Merker, D. / Gerlach, R.G. / Hensel, M. / Muller, Y.A.
History
DepositionMar 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inner membrane protein
E: Inner membrane protein
C: Inner membrane protein
D: Inner membrane protein
B: Inner membrane protein
F: Inner membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8429
Polymers71,5576
Non-polymers2853
Water11,620645
1
A: Inner membrane protein
B: Inner membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0424
Polymers23,8522
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-15 kcal/mol
Surface area11340 Å2
MethodPISA
2
E: Inner membrane protein
F: Inner membrane protein


Theoretical massNumber of molelcules
Total (without water)23,8522
Polymers23,8522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-9 kcal/mol
Surface area11280 Å2
MethodPISA
3
C: Inner membrane protein
D: Inner membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9473
Polymers23,8522
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-14 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.334, 58.360, 65.828
Angle α, β, γ (deg.)93.88, 94.00, 119.00
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Inner membrane protein / Membrane protein / Putative inner membrane or exported protein


Mass: 11926.239 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: siiA, DD95_13055, EIL76_22260 / Production host: Escherichia coli (E. coli) / References: UniProt: H9L4G5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9.1
Details: 0.2 M Sodium phosphate dibasic dihydrate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 29, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.9→42.5 Å / Num. obs: 57795 / % possible obs: 95.9 % / Redundancy: 1.7 % / Biso Wilson estimate: 17.81 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.114 / Net I/σ(I): 7.5
Reflection shellResolution: 1.9→2.01 Å / Mean I/σ(I) obs: 2.3 / CC1/2: 0.72 / Rrim(I) all: 0.54 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→19.964 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.38
RfactorNum. reflection% reflection
Rfree0.2462 2892 5 %
Rwork0.1862 --
obs0.1892 57795 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4826 0 15 645 5486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134942
X-RAY DIFFRACTIONf_angle_d1.116670
X-RAY DIFFRACTIONf_dihedral_angle_d12.4573094
X-RAY DIFFRACTIONf_chiral_restr0.067817
X-RAY DIFFRACTIONf_plane_restr0.007806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8981-1.92920.34191330.34742515X-RAY DIFFRACTION92
1.9292-1.96240.3041370.29492596X-RAY DIFFRACTION97
1.9624-1.99810.29121370.22892593X-RAY DIFFRACTION96
1.9981-2.03650.2781370.21462605X-RAY DIFFRACTION98
2.0365-2.0780.25881360.21082591X-RAY DIFFRACTION97
2.078-2.12310.26511380.21362626X-RAY DIFFRACTION97
2.1231-2.17250.26221380.22616X-RAY DIFFRACTION98
2.1725-2.22670.28681380.23522605X-RAY DIFFRACTION97
2.2267-2.28690.34361350.2622571X-RAY DIFFRACTION97
2.2869-2.3540.26981390.20752638X-RAY DIFFRACTION97
2.354-2.42990.22611400.17552644X-RAY DIFFRACTION98
2.4299-2.51660.25341360.16992594X-RAY DIFFRACTION98
2.5166-2.61710.24081360.17012636X-RAY DIFFRACTION98
2.6171-2.7360.24611390.17312637X-RAY DIFFRACTION98
2.736-2.87980.21561360.17292593X-RAY DIFFRACTION98
2.8798-3.05960.20791410.17052675X-RAY DIFFRACTION98
3.0596-3.29490.23081400.16592630X-RAY DIFFRACTION98
3.2949-3.62470.2261390.15372649X-RAY DIFFRACTION98
3.6247-4.14510.22911420.15132647X-RAY DIFFRACTION98
4.1451-5.20710.19751380.14582628X-RAY DIFFRACTION99
5.2071-19.96550.26321370.19162614X-RAY DIFFRACTION97
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)
12.0514-0.6722-0.47992.1974-0.02853.06840.0510.07050.0595-0.13-0.02330.2021-0.3542-0.3208-0.00260.15880.0586-0.01130.1217-0.00410.1075-28.714350.309731.1979
21.59660.59320.10412.0568-0.24183.0871-0.06860.1031-0.2533-0.11950.13560.03070.64630.0593-0.03180.2480.00510.02380.1187-0.00390.1173-18.149437.39678.3652
32.1166-0.37530.27431.5636-0.22081.9980.13360.1660.2202-0.0024-0.2016-0.25140.01910.6729-0.03910.0583-0.02910.02030.31240.07050.1417-12.306847.44254.2858
42.9558-0.4737-0.19791.7704-0.44013.0043-0.0073-0.13090.05560.0491-0.00070.2484-0.1444-0.7729-0.00160.07810.02380.01840.3153-0.01330.1338-37.211348.023152.5794
51.451-0.5311-0.10153.0478-0.06772.3305-0.1234-0.0841-0.3984-0.03340.0307-0.13410.8930.4013-0.04960.46790.18870.04370.14890.02930.2039-16.106628.353929.5599
62.54260.2349-0.16131.8223-0.32082.6237-0.0117-0.24020.3080.2856-0.1211-0.3242-0.57250.7218-0.04070.254-0.1491-0.04970.3739-0.01010.2-5.788459.13511.7507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 103 through 204)
2X-RAY DIFFRACTION2(chain 'B' and resid 103 through 204)
3X-RAY DIFFRACTION3(chain 'C' and resid 103 through 203)
4X-RAY DIFFRACTION4(chain 'D' and resid 103 through 206)
5X-RAY DIFFRACTION5(chain 'E' and resid 103 through 206)
6X-RAY DIFFRACTION6(chain 'F' and resid 103 through 206)

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