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- PDB-5utt: SrtA sortase from Actinomyces oris -

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Basic information

Entry
Database: PDB / ID: 5utt
TitleSrtA sortase from Actinomyces oris
ComponentsSortase
KeywordsHYDROLASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


Sortase E / : / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesActinomyces oris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOsipiuk, J. / Ma, X. / Ton-That, H. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200700058C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Cell-to-cell interaction requires optimal positioning of a pilus tip adhesin modulated by gram-positive transpeptidase enzymes.
Authors: Chang, C. / Wu, C. / Osipiuk, J. / Siegel, S.D. / Zhu, S. / Liu, X. / Joachimiak, A. / Clubb, R.T. / Das, A. / Ton-That, H.
History
DepositionFeb 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Aug 21, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.4Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sortase
B: Sortase
C: Sortase
D: Sortase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,13516
Polymers83,7094
Non-polymers42512
Water9,530529
1
A: Sortase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0344
Polymers20,9271
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sortase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0344
Polymers20,9271
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sortase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0344
Polymers20,9271
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Sortase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0344
Polymers20,9271
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.183, 75.085, 77.652
Angle α, β, γ (deg.)90.00, 89.96, 90.00
Int Tables number4
Space group name H-MP1211
DetailsMonomer as determined by size exclusion chromatography

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Components

#1: Protein
Sortase


Mass: 20927.277 Da / Num. of mol.: 4 / Fragment: residues 71-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomyces oris (bacteria) / Gene: AXE84_04905 / Plasmid: pMCSG7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: A0A0X8K1J2
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 25% PEG 3350, 0.2 M magnesium chloride, 0.1 M Bis-Tris:HCl buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 2, 2017
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.524
11-h,-k,l20.476
ReflectionResolution: 1.7→37.54 Å / Num. obs: 74465 / % possible obs: 94.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.048 / Rrim(I) all: 0.092 / Χ2: 1.483 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.732.80.6191.9229410.8010.4040.7421.0975.3
1.73-1.762.80.520.820.3470.6281.14288.7
1.76-1.7930.4220.8730.2830.511.1393.8
1.79-1.833.20.3880.9020.2530.4651.17793.9
1.83-1.873.40.3430.9130.2160.4061.25995
1.87-1.913.70.2720.9530.1650.3191.32894.6
1.91-1.963.70.2280.9610.1390.2681.4493.9
1.96-2.023.70.190.9720.1150.2231.55493.4
2.02-2.073.70.1690.9750.1030.1981.55993.8
2.07-2.143.70.1490.980.090.1751.58894.1
2.14-2.223.70.1320.9820.080.1541.59295.2
2.22-2.313.70.120.9850.0730.1411.63297
2.31-2.413.70.1090.9860.0660.1271.68297.3
2.41-2.543.70.0950.990.0590.1121.6498.3
2.54-2.73.70.0910.9890.0550.1061.6698.7
2.7-2.913.80.0770.9910.0460.091.60599
2.91-3.23.80.0660.9940.0390.0771.58599.3
3.2-3.663.80.0540.9960.0320.0631.49999.4
3.66-4.613.80.0430.9970.0260.051.39399.4
4.61-503.70.0440.9970.0270.0521.57698.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
HKL-3000data scaling
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
HKL-3000phasing
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CUW

5cuw


Resolution: 1.7→37.54 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.344 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20454 3651 4.9 %RANDOM
Rwork0.15988 ---
obs0.16202 70787 94.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.422 Å2
Baniso -1Baniso -2Baniso -3
1--17.99 Å2-0 Å20.29 Å2
2--25.41 Å20 Å2
3----7.42 Å2
Refinement stepCycle: 1 / Resolution: 1.7→37.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5620 0 12 529 6161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195792
X-RAY DIFFRACTIONr_bond_other_d0.0010.025337
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9367906
X-RAY DIFFRACTIONr_angle_other_deg0.812312273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29224.397282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2415903
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0291537
X-RAY DIFFRACTIONr_chiral_restr0.0870.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216724
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021357
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_it0.8491.1242886
X-RAY DIFFRACTIONr_mcbond_other0.851.1242885
X-RAY DIFFRACTIONr_mcangle_it1.381.6823603
X-RAY DIFFRACTIONr_mcangle_other1.381.6823604
X-RAY DIFFRACTIONr_scbond_it1.261.2942906
X-RAY DIFFRACTIONr_scbond_other1.261.2942906
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0151.8854298
X-RAY DIFFRACTIONr_long_range_B_refined4.69410.2556712
X-RAY DIFFRACTIONr_long_range_B_other4.569.7236524
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 273 -
Rwork0.232 4113 -
obs--75.48 %
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)
10.47570.11440.0770.12880.01310.33520.0256-0.0109-0.0155-0.0076-0.00980.01270.0048-0.0032-0.01590.0840.0026-0.00320.0008-0.00050.09223.401527.407-5.6553
20.7007-0.1914-0.14340.13050.03310.35680.02630.01390.02860.0022-0.01920.0049-0.0078-0.0088-0.00710.0838-0.00260.00810.00350.00030.090854.512337.3989-13.8112
30.6159-0.17380.16060.14750.03190.27320.02660.0149-0.05090.0122-0.00020.01030.00050.0242-0.02650.08010.0002-0.0040.00350.00260.089535.589627.285625.0389
40.70420.1241-0.12320.1859-0.0170.38650.0281-0.00660.0252-0.005-0.0277-0.00150.00040.0122-0.00040.07720.00460.00630.00490.0020.08354.507137.299433.2912
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A78 - 503
2X-RAY DIFFRACTION2B78 - 503
3X-RAY DIFFRACTION3C78 - 503
4X-RAY DIFFRACTION4D78 - 503

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