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- PDB-4o8l: Structure of sortase A from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 4o8l
TitleStructure of sortase A from Streptococcus pneumoniae
Components(Sortase) x 2
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMisra, A. / Biswas, T. / Das, S. / Marathe, U. / Roy, R.P. / Ramakumar, S.
Citation
Journal: To be Published
Title: Structure of sortase A from Streptococcus pneumoniae
Authors: Misra, A. / Biswas, T. / Das, S. / Marathe, U. / Roy, R.P. / Ramakumar, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization and preliminary X-ray diffraction studies of sortase A from Streptococcus pneumoniae
Authors: Misra, A. / Biswas, T. / Das, S. / Marathe, U. / Sehgal, D. / Roy, R.P. / Ramakumar, S.
History
DepositionDec 28, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release

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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


Theoretical massNumber of molelcules
Total (without water)84,4554
Polymers84,4554
Non-polymers00
Water97354
1
A: Sortase
B: Sortase


Theoretical massNumber of molelcules
Total (without water)42,2362
Polymers42,2362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10300 Å2
ΔGint-60 kcal/mol
Surface area15370 Å2
MethodPISA
2
C: Sortase
D: Sortase


Theoretical massNumber of molelcules
Total (without water)42,2202
Polymers42,2202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11020 Å2
ΔGint-60 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.940, 103.450, 74.870
Angle α, β, γ (deg.)90.000, 115.650, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a dimer. There are 2 such biological units (dimers) present in the asymmetric unit (One dimer is formed by chains A & B and the other by chains C & D).

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Components

#1: Protein Sortase


Mass: 21109.846 Da / Num. of mol.: 3 / Fragment: CATALYTIC DOMAIN, UNP residues 82-247 / Mutation: 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: Protein Sortase


Mass: 21125.846 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, UNP residues 82-247 / Mutation: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.77 Å3/Da / Density % sol: 55.55 % / Mosaicity: 1.52 °
Crystal growTemperature: 293 K / Method: microbatch, under oil / pH: 7
Details: 0.2 M tri-ammonium citrate, pH 7.0, 20% (w/v) PEG 3350, 40% (v/v) 1,3-Butanediol, Microbatch, Under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 8, 2011 / Details: MIRRORS
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→67.492 Å / Num. all: 25168 / Num. obs: 25168 / % possible obs: 99.2 % / Redundancy: 7.5 % / Rsym value: 0.094 / Net I/σ(I): 14.3
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
2.7-2.857.40.5291.52671536210.2060.5293.898.6
2.85-3.027.50.3682.12584034680.1420.3685.398.8
3.02-3.237.50.2223.52421032250.0860.2228.399
3.23-3.497.40.1514.22259430390.0590.15111.699.3
3.49-3.827.50.0967.22087428010.0380.09616.999.5
3.82-4.277.50.0757.81913725590.0290.0752099.7
4.27-4.937.50.0610.11678622310.0240.0624.899.7
4.93-6.047.50.0669.11443619150.0260.06624.199.9
6.04-8.547.50.0569.51116214970.0220.05626.5100
8.54-31.8417.30.0529.559058120.0210.05231.398

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
MAR345dtbdata collection
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→30.71 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2245 / WRfactor Rwork: 0.1727 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8449 / SU B: 23.863 / SU ML: 0.228 / SU R Cruickshank DPI: 0.6869 / SU Rfree: 0.3028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.687 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. Oxidized CYS (CSO) was modeled in place of CYS 207 in Chain B.
RfactorNum. reflection% reflectionSelection details
Rfree0.2339 1273 5.1 %RANDOM
Rwork0.181 ---
obs0.1836 25152 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 139.45 Å2 / Biso mean: 62.0619 Å2 / Biso min: 22.05 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å2-0.13 Å2
2--1.07 Å20 Å2
3----1.85 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5212 0 0 54 5266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195316
X-RAY DIFFRACTIONr_bond_other_d0.0010.025016
X-RAY DIFFRACTIONr_angle_refined_deg1.1621.9687205
X-RAY DIFFRACTIONr_angle_other_deg0.85311556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8415666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.19425.675252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8515926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8571520
X-RAY DIFFRACTIONr_chiral_restr0.0660.2811
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026083
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021153
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 109 -
Rwork0.3 1725 -
all-1834 -
obs--98.55 %
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)
15.6401-1.1375-0.63695.5668-0.0373.51850.11510.1468-0.4567-0.1549-0.11190.2398-0.00460.267-0.00320.0086-0.0012-0.03720.1764-0.04110.2838-4.01071.226215.1816
22.95650.8449-0.51135.8897-0.82864.092-0.10750.18860.30040.1792-0.04060.4395-0.6175-0.12080.14810.19270.0261-0.09510.1696-0.03930.3405-7.505536.220814.52
34.4475-0.4228-0.06978.1657-0.37384.7320.0350.4229-0.0145-0.2511-0.05870.5741-0.3247-0.01140.02370.17340.0178-0.10320.10330.01730.3114-6.4433.009112.9857
44.8934-0.5564-0.17364.18770.11833.1331-0.0769-0.0293-0.6161-0.04450.05120.44220.3653-0.04010.02570.1049-0.0397-0.01110.2735-0.00020.5219-6.7451-1.459417.2852
58.24510.2278-0.21864.5341-0.09863.1290.13390.11680.4415-0.0369-0.1643-0.1496-0.0155-0.33590.03040.07380.03210.01830.35660.01150.413-40.40669.069622.2779
65.6101-0.06793.17257.1222-0.18165.57970.28320.394-0.2554-0.3074-0.2354-0.05920.60960.1398-0.04780.31480.0708-0.01040.2238-0.01970.1957-38.0449-25.44426.333
74.5766-2.15912.12818.0067-2.26183.21890.59920.5682-0.2759-0.5456-0.38640.66850.71690.0362-0.21280.2430.0126-0.06880.1378-0.06150.1949-41.5786-21.101224.4265
85.97190.79440.196.31330.69683.51040.0865-0.07360.56270.1502-0.0092-0.5695-0.1574-0.1354-0.07730.07370.01520.07120.3783-0.00710.4257-36.468110.98623.0631
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A80 - 187
2X-RAY DIFFRACTION2A188 - 247
3X-RAY DIFFRACTION3B92 - 191
4X-RAY DIFFRACTION4B192 - 247
5X-RAY DIFFRACTION5C75 - 187
6X-RAY DIFFRACTION6C188 - 247
7X-RAY DIFFRACTION7D79 - 189
8X-RAY DIFFRACTION8D190 - 247

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