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- PDB-5k9a: Sortase A from Corynebacterium diphtheriae -

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Basic information

Entry
Database: PDB / ID: 5k9a
TitleSortase A from Corynebacterium diphtheriae
ComponentsPutative fimbrial associated sortase-like protein
KeywordsHYDROLASE / sortase / structural genomics / IDP58949 / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


hydrolase activity / membrane
Similarity search - Function
Sortase C / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fimbrial associated sortase-like protein
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOsipiuk, J. / Huang, I.-H. / 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: 2018
Title: In vitro reconstitution of sortase-catalyzed pilus polymerization reveals structural elements involved in pilin cross-linking.
Authors: Chang, C. / Amer, B.R. / Osipiuk, J. / McConnell, S.A. / Huang, I.H. / Hsieh, V. / Fu, J. / Nguyen, H.H. / Muroski, J. / Flores, E. / Ogorzalek Loo, R.R. / Loo, J.A. / Putkey, J.A. / ...Authors: Chang, C. / Amer, B.R. / Osipiuk, J. / McConnell, S.A. / Huang, I.H. / Hsieh, V. / Fu, J. / Nguyen, H.H. / Muroski, J. / Flores, E. / Ogorzalek Loo, R.R. / Loo, J.A. / Putkey, J.A. / Joachimiak, A. / Das, A. / Clubb, R.T. / Ton-That, H.
History
DepositionMay 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2May 30, 2018Group: 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 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.5Sep 27, 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: Putative fimbrial associated sortase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6402
Polymers23,5441
Non-polymers961
Water2,990166
1
A: Putative fimbrial associated sortase-like protein
hetero molecules

A: Putative fimbrial associated sortase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2804
Polymers47,0882
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area2970 Å2
ΔGint-36 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.716, 77.716, 202.282
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Putative fimbrial associated sortase-like protein


Mass: 23544.125 Da / Num. of mol.: 1 / Fragment: UNP resdiues 37-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis) (bacteria)
Strain: ATCC 700971 / NCTC 13129 / Biotype gravis / Gene: DIP2012 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6NF82
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 3.74 Å3/Da / Density % sol: 60.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M ammonium sulfate, 0.1 M MES/NaOH buffer, 10% 1,4-dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→38.9 Å / Num. obs: 21872 / % possible obs: 99.7 % / Redundancy: 15.4 % / Rmerge(I) obs: 0.142 / Net I/av σ(I): 30.661 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.1415.20.9161100
2.14-2.1815.50.8491100
2.18-2.22160.651100
2.22-2.26160.631100
2.26-2.3116.10.5541100
2.31-2.3716.10.5141100
2.37-2.42160.431100
2.42-2.49160.3581100
2.49-2.5616.10.3281100
2.56-2.6515.90.2841100
2.65-2.7415.90.2361100
2.74-2.8515.80.1961100
2.85-2.9815.70.1551100
2.98-3.1415.60.1271100
3.14-3.3315.40.108199.6
3.33-3.5915.10.094199.6
3.59-3.9514.60.084199.6
3.95-4.5214.40.068199.4
4.52-5.713.80.055199.2
5.7-5013.20.046197.4

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0069refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XWG

2xwg


Resolution: 2.1→38.9 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.708 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.127
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 1106 5.1 %RANDOM
Rwork0.1605 ---
obs0.1622 20740 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 97.39 Å2 / Biso mean: 31.335 Å2 / Biso min: 14.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.16 Å2-0 Å2
2--0.33 Å2-0 Å2
3----1.07 Å2
Refinement stepCycle: final / Resolution: 2.1→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1662 0 5 167 1834
Biso mean--66.04 38.48 -
Num. residues----215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191795
X-RAY DIFFRACTIONr_bond_other_d0.0010.021679
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.9692484
X-RAY DIFFRACTIONr_angle_other_deg0.8633887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2285241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62524.94489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48515281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1641511
X-RAY DIFFRACTIONr_chiral_restr0.1010.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212104
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02399
X-RAY DIFFRACTIONr_mcbond_it2.0552.23887
X-RAY DIFFRACTIONr_mcbond_other2.0432.226886
X-RAY DIFFRACTIONr_mcangle_it3.0333.321114
LS refinement shellResolution: 2.102→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 80 -
Rwork0.174 1453 -
all-1533 -
obs--97.77 %
Refinement TLS params.Method: refined / Origin x: 37.3472 Å / Origin y: 6.6678 Å / Origin z: 33.343 Å
111213212223313233
T0.0592 Å2-0.0195 Å2-0.003 Å2-0.0264 Å20.0141 Å2--0.0113 Å2
L0.566 °20.4809 °20.3287 °2-0.4115 °20.2808 °2--1.7126 °2
S-0.0239 Å °0.0616 Å °0.0163 Å °-0.0151 Å °0.0572 Å °0.0177 Å °0.0063 Å °-0.0031 Å °-0.0333 Å °

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