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- PDB-2xwg: Crystal structure of sortase C-1 from Actinomyces oris (formerly ... -

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Basic information

Entry
Database: PDB / ID: 2xwg
TitleCrystal structure of sortase C-1 from Actinomyces oris (formerly Actinomyces naeslundii)
ComponentsSORTASE
KeywordsHYDROLASE / FIMBRIAL ASSEMBLY
Function / homology
Function and homology information


membrane => GO:0016020 / hydrolase activity / metal ion binding
Similarity search - Function
Sortase C / 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: 2.4 Å
AuthorsPersson, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structure of the Sortase Acsrtc-1 from Actinomyces Oris
Authors: Persson, K.
History
DepositionNov 2, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 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 / pdbx_struct_conn_angle / struct_conn / struct_sheet / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _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. THE SHEETS PRESENTED AS "BA" 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. THE SHEETS PRESENTED AS "CA" 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. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -6-STRANDED BARREL THIS IS REPRESENTED BY A -5-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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
E: SORTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,8179
Polymers130,6565
Non-polymers1604
Water3,963220
1
A: SORTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2113
Polymers26,1311
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SORTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1712
Polymers26,1311
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SORTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1712
Polymers26,1311
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SORTASE


Theoretical massNumber of molelcules
Total (without water)26,1311
Polymers26,1311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: SORTASE


Theoretical massNumber of molelcules
Total (without water)26,1311
Polymers26,1311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.070, 108.230, 143.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.7845, -0.4267, -0.4499), (0.2581, -0.8844, 0.3889), (-0.5639, 0.189, 0.804)21.636, 54.5004, -28.3001
2given(0.4229, -0.2829, -0.8609), (-0.2478, -0.9499, 0.1904), (-0.8716, 0.1328, -0.4718)-13.3522, 15.4772, -24.684
3given(-0.977, -0.1644, 0.136), (-0.1064, -0.1766, -0.9785), (0.1849, -0.9704, 0.1551)-9.3367, 36.0191, 31.8539
4given(-0.507, 0.4225, 0.7513), (0.8504, 0.1032, 0.5159), (0.1405, 0.9005, -0.4116)-2.6579, 59.3118, 9.6005

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Components

#1: Protein
SORTASE /


Mass: 26131.248 Da / Num. of mol.: 5 / Fragment: SORTASE, RESIDUES 78-288
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACTINOMYCES ORIS (bacteria) / Strain: T14V / Description: ISOLATED FROM ORAL CAVITY, DENTAL PLAQUE / Plasmid: PET-M11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q0Z952
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 4 Å3/Da / Density % sol: 69.5 % / Description: NONE
Crystal growDetails: 1.9 M NAFORMATE, 1.9 M KFORMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.979
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 12, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→45.5 Å / Num. obs: 62240 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 35.03 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.2 / % possible all: 91.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W1J

2w1j


Resolution: 2.4→43.674 Å / SU ML: 0.32 / σ(F): 0 / Phase error: 26.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 3201 5.2 %
Rwork0.2053 --
obs0.2074 61074 95.59 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.31 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 44.9 Å2
Baniso -1Baniso -2Baniso -3
1-11.7478 Å20 Å20 Å2
2---13.6598 Å20 Å2
3---1.912 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6957 0 4 220 7181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117114
X-RAY DIFFRACTIONf_angle_d1.4129719
X-RAY DIFFRACTIONf_dihedral_angle_d16.3882619
X-RAY DIFFRACTIONf_chiral_restr0.0931151
X-RAY DIFFRACTIONf_plane_restr0.0071252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.435800.28892329X-RAY DIFFRACTION85
2.4358-2.473900.28432374X-RAY DIFFRACTION86
2.4739-2.51440.3223210.27642037X-RAY DIFFRACTION87
2.5144-2.557800.2692498X-RAY DIFFRACTION91
2.5578-2.604300.27042489X-RAY DIFFRACTION90
2.6043-2.65440.30853390.27582137X-RAY DIFFRACTION92
2.6544-2.708600.26622577X-RAY DIFFRACTION94
2.7086-2.76740.29843190.25752282X-RAY DIFFRACTION94
2.7674-2.831800.27742622X-RAY DIFFRACTION96
2.8318-2.90260.30173050.26232354X-RAY DIFFRACTION96
2.9026-2.981100.25882679X-RAY DIFFRACTION98
2.9811-3.06880.27662690.24312427X-RAY DIFFRACTION97
3.0688-3.167800.24372717X-RAY DIFFRACTION98
3.1678-3.2810.28852680.23932459X-RAY DIFFRACTION99
3.281-3.412300.22072735X-RAY DIFFRACTION99
3.4123-3.56750.25312170.1912526X-RAY DIFFRACTION99
3.5675-3.75550.23472120.18872558X-RAY DIFFRACTION100
3.7555-3.99070.21341700.16722613X-RAY DIFFRACTION100
3.9907-4.29850.1861520.15142644X-RAY DIFFRACTION100
4.2985-4.73070.15781370.13312672X-RAY DIFFRACTION100
4.7307-5.41410.20461040.15092708X-RAY DIFFRACTION100
5.4141-6.8170.20682390.19592631X-RAY DIFFRACTION100
6.817-43.68160.24621490.19282805X-RAY DIFFRACTION99
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)
11.0703-0.12610.03681.10480.22271.2087-0.01680.01130.1005-0.1099-0.06330.1704-0.1461-0.2017-00.13990.0147-0.04150.2282-0.02520.2443-16.376231.234816.998
20.4621-0.1048-0.30731.44550.10671.0227-0.0422-0.02650.03280.08240.0410.103-0.02970.012200.146-0.02950.04210.1928-0.01430.1921-1.506745.443544.2046
30.56510.3027-0.15941.0808-0.27780.51010.0657-0.08740.01870.1583-0.04680.0103-0.1383-0.020300.3150.0043-0.11150.2016-0.03820.2324-41.4076-8.9745-13.9231
40.7609-0.38970.08990.88030.62491.7795-0.09910.0847-0.052-0.11730.11520.0043-0.05590.152500.1903-0.06780.01840.2479-0.00740.21984.716116.52261.5494
51.47760.21440.28340.61820.21810.60190.03680.2343-0.2156-0.3570.0067-0.0585-0.2490.142600.4847-0.0374-0.08080.3869-0.08670.3034-15.8577-2.3879-27.5408
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E

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