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- PDB-3tiq: Crystal structure of Staphylococcus aureus SasG G51-E-G52 module -

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Basic information

Entry
Database: PDB / ID: 3tiq
TitleCrystal structure of Staphylococcus aureus SasG G51-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 fold - #30 / 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 fold - #30 / 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 NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8739 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 1.3Sep 13, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Surface protein G
B: Surface protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6638
Polymers47,4192
Non-polymers2446
Water11,458636
1
A: Surface protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8563
Polymers23,7101
Non-polymers1462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Surface protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8075
Polymers23,7101
Non-polymers974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.486, 84.771, 71.689
Angle α, β, γ (deg.)90.00, 100.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Surface protein G /


Mass: 23709.736 Da / Num. of mol.: 2 / Fragment: UNP Residues 419-629
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (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: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 636 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 416-418 IN THIS ENTRY ARE CLONING ARTIFACTS

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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: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M magnesium chloride, 0.1M Bis-Tris, 25% PEG3350, pH 5.5, vapor diffusion sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC Q315 / Detector: CCD / Date: Oct 23, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. all: 44063 / Num. obs: 43216 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.117 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 14.9
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.87-1.990.3673.02237126474190.7
1.99-2.120.2195.22247746595199.9
2.12-2.290.1537.52234316224199.6
2.29-2.510.10610.37213515675199.8
2.51-2.810.07115.39193155137199.7
2.81-3.240.04424.27169834570199.3
3.24-3.960.03532.34141163845199.4
3.96-5.580.03235.99108773007199.3
5.58-500.02836.6262041689197.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
GDAclientdata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TIP

3tip


Resolution: 1.8739→41.297 Å / Occupancy max: 1 / Occupancy min: 0.24 / SU ML: 0.5 / σ(F): 1.34 / Phase error: 30.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2662 2172 5.03 %RANDOM
Rwork0.2052 ---
obs0.2083 43210 98.16 %-
all-44063 --
Solvent computationShrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.452 Å2 / ksol: 0.397 e/Å3
Displacement parametersBiso max: 112.74 Å2 / Biso mean: 42.6828 Å2 / Biso min: 16.7 Å2
Baniso -1Baniso -2Baniso -3
1-5.5243 Å2-0 Å210.7745 Å2
2---0.1464 Å20 Å2
3----5.3779 Å2
Refinement stepCycle: LAST / Resolution: 1.8739→41.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3302 0 13 636 3951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143388
X-RAY DIFFRACTIONf_angle_d1.4344588
X-RAY DIFFRACTIONf_chiral_restr0.105513
X-RAY DIFFRACTIONf_plane_restr0.008609
X-RAY DIFFRACTIONf_dihedral_angle_d14.8841391
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8739-1.91460.32591010.29391990209176
1.9146-1.95910.34111290.25922591272099
1.9591-2.00810.30831440.243125672711100
2.0081-2.06240.27791360.227426092745100
2.0624-2.12310.29241210.225825792700100
2.1231-2.19160.30951460.220126182764100
2.1916-2.270.26531140.221526252739100
2.27-2.36080.31671450.225425832728100
2.3608-2.46830.29211400.232825842724100
2.4683-2.59840.28271330.228126122745100
2.5984-2.76120.28661500.243325932743100
2.7612-2.97430.27321490.217525922741100
2.9743-3.27350.28761560.204425982754100
3.2735-3.74690.2561410.202626112752100
3.7469-4.71960.24331390.165926272766100
4.7196-41.30690.20381280.17232659278799
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)
11.1349-0.1662-2.50250.63481.33118.1740.36390.27770.2956-0.38380.1632-0.2548-0.4699-0.0289-0.42070.41840.07080.09330.36690.02370.347529.7533-39.0483-55.7048
21.14960.0699-2.0619-0.29290.16345.98220.04340.1192-0.0901-0.14560.0239-0.12010.0102-0.193-0.02160.47220.05150.11040.27590.02130.335832.2168-39.8667-63.5263
30.4483-0.3681-0.32271.40871.73474.62720.0134-0.05090.0455-0.00150.1366-0.1217-0.14890.0418-0.10780.23540.02990.01920.2165-0.01260.312716.2007-26.6262-8.3534
40.31740.3371-1.9464-0.076-0.82998.14990.4231-0.24920.30080.20530.19430.1293-0.73590.3289-0.59580.565-0.05560.08130.3605-0.06720.320111.0651-14.14956.2116
50.5917-0.0596-1.85680.18890.82497.44230.0914-0.11960.00410.0301-0.11590.0875-0.72660.2978-0.02660.56490.0030.13070.23330.0240.398512.739-16.436840.7421
60.06680.48260.01130.9446-0.6040.08150.43010.12050.38960.3929-0.05510.0461-0.9610.0261-0.42270.4650.06220.12580.5150.09570.3502-28.9054-41.715387.8004
71.88850.361-4.4865-0.2766-1.41777.2141-0.1466-0.2402-0.0384-0.2134-0.2129-0.13350.17090.80030.28220.3922-0.04520.12050.51730.06040.4073-29.6121-44.014790.8188
82.5407-0.3405-0.56922.3185-1.28753.34050.09160.1029-0.1348-0.2872-0.02310.0732-0.0185-0.6966-0.14960.2420.05520.00090.34330.02840.2431-8.4689-25.401839.0404
92.252-0.5139-0.53292.7813-0.75413.47970.4317-0.58260.14020.6616-0.301-0.1475-0.41810.57080.02470.4274-0.1223-0.02610.48160.02170.2408-0.3865-10.6626-21.3373
100.50320.29331.05780.2332-0.16112.7338-0.05680.5011-0.0281-0.64450.74420.06160.21011.4676-0.18430.7060.12040.05550.75120.12240.3113-1.4605-17.06510.2831
113.46520.1245-3.30372.39110.52048.15260.29130.00030.0347-0.0175-0.2871-0.2527-0.1331-0.18510.03050.26590.0134-0.00980.23930.03430.24051.5654-11.4843-31.0928
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 6:35)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 36:83)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 84:140)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 141:163)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 164:215)A0
6X-RAY DIFFRACTION6chain 'B' and (resseq 2:35)B0
7X-RAY DIFFRACTION7chain 'B' and (resseq 36:83)B0
8X-RAY DIFFRACTION8chain 'B' and (resseq 84:140)B0
9X-RAY DIFFRACTION9chain 'B' and (resseq 141:179)B0
10X-RAY DIFFRACTION10chain 'B' and (resseq 180:202)B0
11X-RAY DIFFRACTION11chain 'B' and (resseq 203:215)B0

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