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- PDB-3tip: Crystal structure of Staphylococcus aureus SasG E-G52 module -

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Basic information

Entry
Database: PDB / ID: 3tip
TitleCrystal structure of Staphylococcus aureus SasG E-G52 module
ComponentsSurface protein G
KeywordsSTRUCTURAL PROTEIN / single-layer beta sheet / biofilm formation / surface
Function / homology
Function and homology information


single-species submerged biofilm formation / extracellular region
Similarity search - Function
Resuscitation-promoting factor rpfb. / Resuscitation-promoting factor rpfb fold / E domain / E domain / Bacterial lectin / G5 domain / G5 domain / G5 domain profile. / G5 / YSIRK type signal peptide ...Resuscitation-promoting factor rpfb. / Resuscitation-promoting factor rpfb fold / E domain / E domain / Bacterial lectin / G5 domain / G5 domain / G5 domain profile. / G5 / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7009 Å
AuthorsGruszka, D.T. / Wojdyla, J.A. / Turkenburg, J.P. / Potts, J.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Staphylococcal biofilm-forming protein has a contiguous rod-like structure.
Authors: Gruszka, D.T. / Wojdyla, J.A. / Bingham, R.J. / Turkenburg, J.P. / Manfield, I.W. / Steward, A. / Leech, A.P. / Geoghegan, J.A. / Foster, T.J. / Clarke, J. / Potts, J.R.
History
DepositionAug 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2May 9, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Surface protein G


Theoretical massNumber of molelcules
Total (without water)14,4931
Polymers14,4931
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.813, 34.721, 55.821
Angle α, β, γ (deg.)90.00, 99.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Surface protein G /


Mass: 14493.204 Da / Num. of mol.: 1 / Fragment: UNP Residues 498-629
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: NCTC 8325 / Gene: SAOUHSC_02798, sasG / Plasmid: pSKB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q2G2B2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 498-501 IN THIS ENTRY ARE CLONING ARTIFACT

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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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.2M ammonium chloride, 20% PEG3350, pH 7.4, vapor diffusion sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9794, 0.9763, 0.9797
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97631
30.97971
ReflectionResolution: 1.7009→55.05 Å / Num. all: 15482 / Num. obs: 15482 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Rsym value: 0.06 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7009-1.7940.6791.1890022130.67998.5
1.79-1.94.10.3642.1862821040.364100
1.9-2.034.10.1854.2829520320.18599.9
2.03-2.24.10.1266762118640.126100
2.2-2.414.10.1027.3698417060.10299.8
2.41-2.694.10.0799.4645915740.07999.9
2.69-3.114.10.04713.1561413790.04799.9
3.11-3.840.03416.1464611630.03499.8
3.8-5.3840.02327.137389230.023100
5.38-34.7213.90.02228.720455240.02298.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
GDAclientdata collection
XDSdata reduction
MADSYSphasing
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7009→29.368 Å / Occupancy max: 1 / Occupancy min: 0.32 / SU ML: 0.45 / σ(F): 1.36 / Phase error: 29.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 1186 7.69 %RANDOM
Rwork0.1965 ---
obs0.1999 15431 99.39 %-
all-15482 --
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.845 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso max: 86.37 Å2 / Biso mean: 30.6112 Å2 / Biso min: 11.82 Å2
Baniso -1Baniso -2Baniso -3
1--7.3125 Å20 Å26.0013 Å2
2--12.5207 Å20 Å2
3----5.2083 Å2
Refinement stepCycle: LAST / Resolution: 1.7009→29.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1018 0 0 215 1233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111052
X-RAY DIFFRACTIONf_angle_d1.5561426
X-RAY DIFFRACTIONf_chiral_restr0.095155
X-RAY DIFFRACTIONf_plane_restr0.008193
X-RAY DIFFRACTIONf_dihedral_angle_d15.064430
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7009-1.77830.37391370.30971735187298
1.7783-1.87210.30581510.247417621913100
1.8721-1.98930.29641440.2091778192299
1.9893-2.14290.24721360.20251778191499
2.1429-2.35850.2911350.204917821917100
2.3585-2.69950.25921710.215517731944100
2.6995-3.40030.26941610.189217901951100
3.4003-29.37190.15981510.16618471998100
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)
12.15190.2502-1.57820.75180.43462.03450.02490.1402-0.12120.0625-0.1632-0.05850.07380.09660.11940.18990.0199-0.03420.20380.03270.15445.991115.896630.2646
25.6057-2.8686-5.87611.86593.06496.16130.217-0.50490.1862-0.15710.141-0.0533-0.28180.4821-0.23910.2355-0.04980.02060.4267-0.11990.294512.074217.435427.1791
31.255-1.23130.01082.79341.91993.28030.1150.1956-0.0328-0.26620.0086-0.0249-0.0955-0.2835-0.18410.22630.0550.00130.18210.06680.256219.51169.941316.2697
45.78650.8055-2.94551.7485-0.6234.96810.17650.11790.2640.13890.230.2201-0.0189-0.3046-0.29240.1759-0.01740.00570.18140.02170.1818-4.996918.483637.7957
57.281.0861-6.97440.4688-0.99836.6897-0.79541.3224-0.1911-0.03780.30940.13040.44710.16310.35040.2778-0.03690.08330.8139-0.0220.3626-30.240616.195152.4695
64.8792-0.2759-4.11320.87640.3953.494-0.1727-0.2936-0.2611-0.3037-0.1679-0.3480.33620.80010.38610.27380.06540.04420.25010.07610.2438-45.423915.831872.0949
72.3683-1.09831.25980.5108-0.59441.42470.0925-0.96940.4621-0.0552-0.2063-0.11120.1683-0.40090.08130.22870.0106-0.00080.3163-0.10090.2032-57.209322.081281.5751
84.8084-0.0974-2.71651.67270.39314.91920.13440.34150.3083-0.2941-0.1076-0.1181-0.4894-0.3093-0.04110.19740.0456-0.01020.14720.06410.1915-48.751421.234167.6323
94.0748-0.5537-2.89020.41040.02982.4311-0.13430.22620.31060.14930.45180.26280.1658-0.5658-0.10650.23620.01490.08770.28240.03430.302-19.280916.292649.0188
105.74920.4506-3.7241.1822-0.05555.76360.203-0.11210.1554-0.091-0.1265-0.14470.0696-0.0077-0.05110.14760.01430.00550.14020.01330.1514-49.172518.413374.639
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:21)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 22:32)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 33:45)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 46:57)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 58:64)A0
6X-RAY DIFFRACTION6chain 'A' and (resseq 65:72)A0
7X-RAY DIFFRACTION7chain 'A' and (resseq 73:80)A0
8X-RAY DIFFRACTION8chain 'A' and (resseq 81:89)A0
9X-RAY DIFFRACTION9chain 'A' and (resseq 90:119)A0
10X-RAY DIFFRACTION10chain 'A' and (resseq 120:132)A0

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