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- PDB-8t28: The crystal structure of SrtC2 sortase from Actinomyces oris -

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Basic information

Entry
Database: PDB / ID: 8t28
TitleThe crystal structure of SrtC2 sortase from Actinomyces oris
ComponentsClass C sortase
KeywordsHYDROLASE / structural genomics / Center for Structural Biology of Infectious Diseases / CSBID
Function / homologySortase C / Sortase family / Sortase domain superfamily / Sortase domain / hydrolase activity / membrane / PHOSPHATE ION / Class C sortase
Function and homology information
Biological speciesActinomyces oris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOsipiuk, J. / Chang, C. / Ton-That, H.L. / Ton-That, H. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00035 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Molecular basis for dual functions in pilus assembly modulated by the lid of a pilus-specific sortase.
Authors: Chang, C. / Ton-That, H. / Osipiuk, J. / Joachimiak, A. / Das, A. / Ton-That, H.
History
DepositionJun 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Class C sortase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2475
Polymers23,9861
Non-polymers2614
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.390, 90.390, 101.704
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-501-

PO4

21A-502-

PO4

31A-503-

CL

41A-504-

CL

51A-688-

HOH

61A-706-

HOH

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Components

#1: Protein Class C sortase


Mass: 23985.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Three N-terminal residues, SNA, are expression tag (cloning artifact)
Source: (gene. exp.) Actinomyces oris (bacteria) / Gene: CYJ23_09785 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2I1IT56
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M Sodium Chloride, 0.1 M Na2HPO4:Citric Acid, 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→45.24 Å / Num. obs: 14868 / % possible obs: 99.7 % / Redundancy: 20.2 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.027 / Rrim(I) all: 0.127 / Χ2: 1.174 / Net I/av σ(I): 25.8 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.1-2.146.71.1561.087020.5040.8190.4611.2570.82196.8
2.14-2.187.91.17140.4620.7950.4061.1820.90199
2.18-2.229.40.9147210.6770.8980.3110.9710.88799.9
2.22-2.2610.90.8297340.7370.9210.2610.8730.999.7
2.26-2.3112.80.8047220.8250.9510.2330.840.901100
2.31-2.3714.90.6887220.8830.9690.1840.7140.98299.9
2.37-2.4217.60.5677300.940.9840.1380.5850.975100
2.42-2.4922.60.5177330.970.9920.110.5290.995100
2.49-2.5626.30.4537300.9780.9950.090.4621.078100
2.56-2.6526.10.3747240.9880.9970.0740.3811.113100
2.65-2.7425.80.3257460.9860.9970.0650.3311.156100
2.74-2.8524.80.2687310.990.9970.0550.2741.232100
2.85-2.9824.40.2187370.9920.9980.0450.2231.245100
2.98-3.1426.10.1787490.9960.9990.0350.1821.35799.9
3.14-3.3325.50.1417480.9970.9990.0280.1431.441100
3.33-3.5923.60.1177490.9970.9990.0240.1191.439100
3.59-3.9525.70.0927590.99810.0180.0941.43100
3.95-4.5224.80.0747700.99910.0150.0761.33699.9
4.52-5.724.10.0617860.99910.0130.0631.13499.9
5.7-45.2421.50.049861110.0110.051.00399.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
HKL-3000data scaling
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.24 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.269 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20098 764 5.1 %RANDOM
Rwork0.16688 ---
obs0.16861 14075 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.069 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å2-0 Å2
3----0.39 Å2
Refinement stepCycle: 1 / Resolution: 2.1→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 12 108 1510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121418
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161324
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.6431930
X-RAY DIFFRACTIONr_angle_other_deg0.4911.5513089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0865185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.036107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28310240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021596
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02240
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2532.91743
X-RAY DIFFRACTIONr_mcbond_other2.2532.91743
X-RAY DIFFRACTIONr_mcangle_it3.0894.347927
X-RAY DIFFRACTIONr_mcangle_other3.0884.353928
X-RAY DIFFRACTIONr_scbond_it3.8293.309675
X-RAY DIFFRACTIONr_scbond_other3.7923.299668
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5324.78992
X-RAY DIFFRACTIONr_long_range_B_refined6.75637.4971472
X-RAY DIFFRACTIONr_long_range_B_other6.71936.8171447
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 65 -
Rwork0.298 985 -
obs--97.49 %
Refinement TLS params.Method: refined / Origin x: -7.0517 Å / Origin y: 37.0297 Å / Origin z: 34.538 Å
111213212223313233
T0.0653 Å2-0.0255 Å20.0304 Å2-0.0147 Å2-0.0144 Å2--0.0231 Å2
L1.7013 °20.2718 °20.381 °2-1.6826 °20.1602 °2--1.8227 °2
S-0.0471 Å °0.0433 Å °-0.123 Å °-0.0294 Å °0.0257 Å °-0.0957 Å °0.1477 Å °0.0263 Å °0.0214 Å °

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