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- PDB-4o8t: Structure of sortase A C207A mutant from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 4o8t
TitleStructure of sortase A C207A mutant from Streptococcus pneumoniae
ComponentsSortase
KeywordsHYDROLASE / 8-stranded beta barrel / sortase-fold / cysteine transpeptidase
Function / homology
Function and homology information


cysteine-type peptidase activity / proteolysis
Similarity search - Function
Sortase A / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsMisra, A. / Biswas, T. / Das, S. / Marathe, U. / Roy, R.P. / Ramakumar, S.
CitationJournal: To be Published
Title: Structure of sortase A C207A mutant from Streptococcus pneumoniae
Authors: Misra, A. / Biswas, T. / Das, S. / Marathe, U. / Roy, R.P. / Ramakumar, S.
History
DepositionDec 30, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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_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: Sortase
B: Sortase
C: Sortase
D: Sortase
E: Sortase
F: Sortase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,5597
Polymers126,4676
Non-polymers921
Water4,216234
1
A: Sortase
B: Sortase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2483
Polymers42,1562
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11040 Å2
ΔGint-66 kcal/mol
Surface area15370 Å2
MethodPISA
2
C: Sortase
D: Sortase


Theoretical massNumber of molelcules
Total (without water)42,1562
Polymers42,1562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11270 Å2
ΔGint-61 kcal/mol
Surface area16110 Å2
MethodPISA
3
E: Sortase
F: Sortase


Theoretical massNumber of molelcules
Total (without water)42,1562
Polymers42,1562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-64 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.570, 113.330, 81.340
Angle α, β, γ (deg.)90.000, 90.800, 90.000
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is a dimer. There are 3 such biological units (dimers) in the asymmetric unit (One dimer is formed by chains A & B, the second one by chains C & D and the third dimer by chains E & F).

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Components

#1: Protein
Sortase /


Mass: 21077.781 Da / Num. of mol.: 6 / Fragment: CATALYTIC DOMAIN, UNP residues 82-247 / Mutation: C207A, T176A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: ATCC BAA-255 / R6 / Gene: sortase A, spr1098, srtA / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8DPM3, sortase A
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.83 Å3/Da / Density % sol: 56.61 % / Mosaicity: 0.93 °
Crystal growTemperature: 293 K / Method: microbatch, under oil / pH: 7
Details: 0.2M tri-ammonium citrate pH 7.0, 20%(w/v) PEG3350, 1.0M Guanidine hydrochloride, Microbatch, Under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9772 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 23, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 2.48→91.598 Å / Num. all: 50010 / Num. obs: 50010 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rsym value: 0.092 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.48-2.614.10.5471.42947372450.3110.5472.599.7
2.61-2.774.20.38922865368880.2180.3893.6100
2.77-2.964.20.262.92704264750.1460.265.1100
2.96-3.24.20.1574.72530360420.0880.1577.8100
3.2-3.514.20.0967.62322355420.0540.09611.8100
3.51-3.924.20.06111.12117750440.0340.06116.9100
3.92-4.534.20.04713.11869544600.0260.04720.9100
4.53-5.554.20.05211.41568837450.0290.05221.3100
5.55-7.844.10.06681204629360.0370.06618.8100
7.84-47.15140.03811.4660116330.0220.03823.399.6

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FN5

3fn5


Resolution: 2.48→46.5 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2115 / WRfactor Rwork: 0.1724 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8392 / SU B: 16.306 / SU ML: 0.179 / SU R Cruickshank DPI: 0.3481 / SU Rfree: 0.2357 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.348 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 2535 5.1 %RANDOM
Rwork0.1824 ---
obs0.1846 49987 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.71 Å2 / Biso mean: 44.8676 Å2 / Biso min: 13.05 Å2
Baniso -1Baniso -2Baniso -3
1--3.94 Å20 Å2-1.05 Å2
2--1.45 Å20 Å2
3---2.5 Å2
Refinement stepCycle: LAST / Resolution: 2.48→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8012 0 6 234 8252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198161
X-RAY DIFFRACTIONr_bond_other_d0.0010.027730
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.96711052
X-RAY DIFFRACTIONr_angle_other_deg0.869317805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87551021
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14425.707382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.746151425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0671530
X-RAY DIFFRACTIONr_chiral_restr0.0710.21243
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219320
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021760
LS refinement shellResolution: 2.48→2.544 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 204 -
Rwork0.284 3473 -
all-3677 -
obs--99.41 %
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)
12.2728-1.327-1.40621.21540.56152.2585-0.0476-0.15220.053-0.14730.0119-0.09770.0924-0.07910.03570.4777-0.05110.08610.2577-0.01980.02188.8877-42.132424.142
21.82970.12220.68130.8050.8641.9405-0.0641-0.089-0.21630.0556-0.0060.04660.0278-0.10510.07010.39550.01990.05870.2665-0.03860.0537-23.1744-41.075912.0686
32.52250.4703-0.07951.17790.64011.6793-0.1493-0.0126-0.20080.0246-0.04280.04190.07930.03430.1920.46130.0360.08610.2691-0.02380.0504-19.5292-41.411711.5948
42.4023-0.3769-1.21420.67560.00871.87840.0216-0.3667-0.027-0.0270.1292-0.0769-0.0116-0.0184-0.15070.41680.00650.03650.3201-0.02620.05359.8428-40.395428.3747
50.457-1.0333-0.21932.7673-0.11071.1720.1317-0.08110.0692-0.19850.1338-0.0896-0.1782-0.05-0.26550.4489-0.05710.11560.22750.05690.1405-53.2064-10.431714.4681
60.8702-0.66880.18911.82070.19780.8598-0.07490.082-0.0310.25030.24420.22370.05730.1396-0.16930.44440.0490.07180.2049-0.02970.1324-21.4476-13.964827.9912
70.27080.26980.00392.96550.72641.1068-0.01120.08770.04680.1890.14870.21990.03670.104-0.13750.42090.0440.11480.2095-0.02510.1007-23.2412-9.884227.1792
82.5305-0.01250.08311.88260.23830.39550.2099-0.1389-0.2106-0.2224-0.00920.022-0.12970.0187-0.20070.4563-0.02670.08070.18670.00270.1273-55.3819-14.764313.3344
91.82040.89830.0141.2847-0.73210.9720.03920.21110.12020.1544-0.00650.19060.00230.1863-0.03270.42440.01980.10380.2547-0.03490.0705-9.1414.930117.2794
101.84-0.57051.03350.59480.14111.7972-0.00030.13020.02270.0687-0.18120.0295-0.11270.21440.18150.3571-0.0680.08580.30750.14350.132523.695813.59825.2792
111.2668-0.45910.75241.3288-1.0461.5217-0.0017-0.0941-0.04470.0062-0.11330.03280.08320.04170.11510.40250.00110.11380.27720.10580.107220.423811.020627.6192
123.40150.11120.60941.3158-0.21261.0941-0.05230.44870.06580.040.1120.16240.02650.1119-0.05970.3556-0.04780.06720.31420.00670.0349-10.184716.307213.3466
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A75 - 188
2X-RAY DIFFRACTION2A189 - 247
3X-RAY DIFFRACTION3B91 - 189
4X-RAY DIFFRACTION4B190 - 247
5X-RAY DIFFRACTION5C73 - 189
6X-RAY DIFFRACTION6C190 - 247
7X-RAY DIFFRACTION7D74 - 188
8X-RAY DIFFRACTION8D189 - 247
9X-RAY DIFFRACTION9E74 - 185
10X-RAY DIFFRACTION10E186 - 247
11X-RAY DIFFRACTION11F74 - 192
12X-RAY DIFFRACTION12F193 - 247

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