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- PDB-4d7w: Crystal structure of sortase C1 (SrtC1) from Streptococcus agalactiae -

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Basic information

Entry
Database: PDB / ID: 4d7w
TitleCrystal structure of sortase C1 (SrtC1) from Streptococcus agalactiae
ComponentsSORTASE FAMILY PROTEIN
KeywordsHYDROLASE / PILUS / GRAM-POSITIVE
Function / homology
Function and homology information


Sortase C / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Sortase family protein / :
Similarity search - Component
Biological speciesSTREPTOCOCCUS AGALACTIAE COH1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMalito, E. / Lazzarin, M. / Cozzi, R. / Bottomley, M.J.
CitationJournal: Faseb J. / Year: 2015
Title: Noncanonical Sortase-Mediated Assembly of Pilus Type 2B in Group B Streptococcus.
Authors: Lazzarin, M. / Cozzi, R. / Malito, E. / Martinelli, M. / D'Onofrio, M. / Maione, D. / Margarit, I. / Rinaudo, C.D.
History
DepositionNov 28, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 2.0Sep 27, 2017Group: Atomic model / Data collection / Category: atom_site / diffrn_detector
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _diffrn_detector.type
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SORTASE FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7082
Polymers23,6461
Non-polymers621
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.560, 124.760, 45.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein SORTASE FAMILY PROTEIN / SORTASE C1


Mass: 23645.752 Da / Num. of mol.: 1 / Fragment: RESIDUES 38-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS AGALACTIAE COH1 (bacteria)
Plasmid: PET15 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: X5KHM5, UniProt: A0A0M3KKU7*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTIGR ANNOTATION OLD LOCUS TAG SAN_1517, LOCUS TAG GBSCOH1_1278 (NCBI PROTEIN ID ACCESSION NUMBER CDN66744)

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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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 9.7
Details: 0.05M TRI-SODIUM CITRATE, 0.05 M BIS-TRIS PROPANE PH 9.7, 16% PEG-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 29, 2014
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→45.9 Å / Num. obs: 16211 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 34.58 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.7
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.8 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4G1J

4g1j


Resolution: 1.95→45.92 Å / SU ML: 0.25 / σ(F): 1.37 / Phase error: 24.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2227 810 5 %
Rwork0.1798 --
obs0.182 16201 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.1 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 44 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 4 90 1645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081585
X-RAY DIFFRACTIONf_angle_d1.0322139
X-RAY DIFFRACTIONf_dihedral_angle_d12.599602
X-RAY DIFFRACTIONf_chiral_restr0.041237
X-RAY DIFFRACTIONf_plane_restr0.005273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.07220.33981310.26742480X-RAY DIFFRACTION97
2.0722-2.23220.27071330.23172521X-RAY DIFFRACTION99
2.2322-2.45680.27221330.21792545X-RAY DIFFRACTION99
2.4568-2.81230.25331340.20722549X-RAY DIFFRACTION99
2.8123-3.5430.28631360.18262594X-RAY DIFFRACTION99
3.543-45.93270.1521430.14392702X-RAY DIFFRACTION98
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)
11.8754-1.0616-0.80320.978-0.80524.96150.30670.11340.82010.3011-0.0128-0.7556-1.13330.29860.38210.3444-0.1062-0.04540.4187-0.00530.670125.279228.854717.5872
20.51830.0621-0.10410.8446-0.38791.0370.0645-0.4955-0.30590.5009-0.279-0.22610.207-0.0719-0.00470.3643-0.06960.010.43730.05790.294410.122617.786224.6742
30.3739-0.2254-0.18110.3545-0.07480.41950.15020.05280.2016-0.1242-0.22020.5701-0.2677-0.51460.00110.25260.028-0.01690.4141-0.05030.3868-0.26323.694415.7558
42.51030.09630.53642.09110.70823.361-0.0230.30840.2963-0.3873-0.0158-0.0474-0.1356-0.03460.00020.26190.00880.00940.26740.06470.265213.708122.05029.5884
50.1810.05980.26710.23140.21640.46680.12660.40860.2023-0.6299-0.2829-0.50770.03590.55280.00020.64340.06310.04970.58570.10020.443917.712117.759-3.9533
60.1061-0.14820.00570.2382-0.04120.04090.25620.09-0.26240.4490.2511-0.63431.21910.68660.00060.38470.0768-0.0140.3734-0.00060.371120.689815.209812.9735
70.99720.02890.24810.4163-0.70471.21960.1902-0.3191-0.2485-0.1727-0.1161-0.11891.028-0.46910.02520.5440.0782-0.01640.38-0.04920.293513.06049.05825.4272
80.64560.0027-0.49120.039-0.08920.5475-0.04650.6728-0.4208-0.58260.0963-0.08070.6464-0.19890.00380.5012-0.0876-0.01930.40690.01310.3690.88239.18485.7522
90.6070.1235-0.50550.40180.42211.0960.10310.3717-0.1847-0.11160.09490.1940.16920.03240.00060.45580.0236-0.00530.38960.00270.371711.680712.51981.3867
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 39 THROUGH 53 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 54 THROUGH 74 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 75 THROUGH 90 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 91 THROUGH 147 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 148 THROUGH 168 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 169 THROUGH 176 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 177 THROUGH 190 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 191 THROUGH 203 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 204 THROUGH 231 )

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