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- PDB-5a0g: N-terminal thioester domain of surface protein from Clostridium p... -

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Basic information

Entry
Database: PDB / ID: 5a0g
TitleN-terminal thioester domain of surface protein from Clostridium perfringens
ComponentsSURFACE ANCHORED PROTEIN
KeywordsCELL ADHESION / SURFACE-ASSOCIATED PROTEIN / GRAM-POSITIVE / ADHESIN / INTERNAL THIOESTER / THIOESTER DOMAIN
Function / homology
Function and homology information


membrane / metal ion binding
Similarity search - Function
Thioester domain / T-Q ester bond containing domain / T-Q ester bond containing domain / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain / SH3 type barrels. / Roll ...Thioester domain / T-Q ester bond containing domain / T-Q ester bond containing domain / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain / SH3 type barrels. / Roll / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Putative surface anchored protein
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsWalden, M. / Edwards, J.M. / Dziewulska, A.M. / Kan, S.-Y. / Schwarz-Linek, U. / Banfield, M.J.
CitationJournal: Elife / Year: 2015
Title: An internal thioester in a pathogen surface protein mediates covalent host binding.
Authors: Walden, M. / Edwards, J.M. / Dziewulska, A.M. / Bergmann, R. / Saalbach, G. / Kan, S.Y. / Miller, O.K. / Weckener, M. / Jackson, R.J. / Shirran, S.L. / Botting, C.H. / Florence, G.J. / ...Authors: Walden, M. / Edwards, J.M. / Dziewulska, A.M. / Bergmann, R. / Saalbach, G. / Kan, S.Y. / Miller, O.K. / Weckener, M. / Jackson, R.J. / Shirran, S.L. / Botting, C.H. / Florence, G.J. / Rohde, M. / Banfield, M.J. / Schwarz-Linek, U.
History
DepositionApr 20, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Mar 22, 2017Group: Database references
Revision 1.3Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _pdbx_database_status.status_code_sf
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 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-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 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-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 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-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 7-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 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-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: SURFACE ANCHORED PROTEIN
B: SURFACE ANCHORED PROTEIN
C: SURFACE ANCHORED PROTEIN
D: SURFACE ANCHORED PROTEIN
E: SURFACE ANCHORED PROTEIN
F: SURFACE ANCHORED PROTEIN


Theoretical massNumber of molelcules
Total (without water)127,7106
Polymers127,7106
Non-polymers00
Water64936
1
A: SURFACE ANCHORED PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,2851
Polymers21,2851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SURFACE ANCHORED PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,2851
Polymers21,2851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SURFACE ANCHORED PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,2851
Polymers21,2851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SURFACE ANCHORED PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,2851
Polymers21,2851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: SURFACE ANCHORED PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,2851
Polymers21,2851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: SURFACE ANCHORED PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,2851
Polymers21,2851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.820, 74.360, 82.810
Angle α, β, γ (deg.)107.32, 104.32, 98.63
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A101 - 274
2010B101 - 274
1020A101 - 274
2020C101 - 274
1030A101 - 275
2030D101 - 275
1040A101 - 275
2040E101 - 275
1050A101 - 275
2050F101 - 275
1060B101 - 274
2060C101 - 274
1070B101 - 274
2070D101 - 274
1080B101 - 274
2080E101 - 274
1090B101 - 274
2090F101 - 274
10100C101 - 274
20100D101 - 274
10110C101 - 274
20110E101 - 274
10120C101 - 274
20120F101 - 274
10130D101 - 275
20130E101 - 275
10140D101 - 275
20140F101 - 275
10150E101 - 275
20150F101 - 275

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
SURFACE ANCHORED PROTEIN


Mass: 21284.984 Da / Num. of mol.: 6 / Fragment: THIOESTER DOMAIN, RESIDUES 92-277
Source method: isolated from a genetically manipulated source
Details: INTERNAL THIOESTER LINKAGE BETWEEN CYS138 AND GLN267
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Strain: B / Plasmid: POPIN-F / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1R775
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.07 Å3/Da / Density % sol: 59.94 % / Description: NONE
Crystal growDetails: 0.2 M TRI-POTASSIUM CITRATE, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Nov 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.62→44.88 Å / Num. obs: 44689 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.5
Reflection shellResolution: 2.62→2.69 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.8 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→44.88 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 25.037 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.498 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.22611 2203 4.9 %RANDOM
Rwork0.19645 ---
obs0.19795 42485 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20.86 Å2-2.81 Å2
2---1.1 Å2-2.01 Å2
3---3.21 Å2
Refinement stepCycle: LAST / Resolution: 2.62→44.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8260 0 0 36 8296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.028428
X-RAY DIFFRACTIONr_bond_other_d0.0070.027777
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.96411444
X-RAY DIFFRACTIONr_angle_other_deg1.2373.00117824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56951046
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.95925.231390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.956151386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4021530
X-RAY DIFFRACTIONr_chiral_restr0.0890.21310
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029644
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021922
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_it2.2133.234202
X-RAY DIFFRACTIONr_mcbond_other2.213.234201
X-RAY DIFFRACTIONr_mcangle_it3.4164.8455242
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7893.4334226
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A100600.07
12B100600.07
21A101150.07
22C101150.07
31A99040.06
32D99040.06
41A102730.06
42E102730.06
51A100710.06
52F100710.06
61B98910.07
62C98910.07
71B95920.07
72D95920.07
81B99590.07
82E99590.07
91B96020.08
92F96020.08
101C99450.06
102D99450.06
111C101520.05
112E101520.05
121C100290.07
122F100290.07
131D99660.06
132E99660.06
141D99140.06
142F99140.06
151E99920.06
152F99920.06
LS refinement shellResolution: 2.62→2.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 151 -
Rwork0.351 3115 -
obs--97.38 %
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)
12.5669-0.7072-0.56572.7634-0.35992.09830.0118-0.0755-0.0801-0.0844-0.00040.29310.2657-0.1242-0.01140.102-0.0841-0.00370.08310.02610.2061-18.8749-16.9364-26.6956
22.8257-0.0943-1.02242.2939-0.45922.94320.0366-0.01070.2769-0.02630.050.0605-0.1946-0.0036-0.08660.0622-0.05170.03520.06380.00020.2175-16.2587-0.8666-27.3331
32.6858-0.07310.29131.7077-0.26942.6937-0.1734-0.02180.1140.1451-0.0234-0.1714-0.3802-0.02330.19680.1047-0.03830.0040.0662-0.00530.178-49.810622.3575-28.7041
42.7826-0.12540.20221.6024-0.10842.4988-0.2532-0.0212-0.3878-0.02890.0576-0.05660.4132-0.11820.19560.1312-0.06770.10460.10110.00160.2391-52.57686.3204-30.611
53.1794-0.0857-0.07220.99180.51722.43550.00050.00240.10760.16220.03510.0798-0.1713-0.1973-0.03570.17220.0070.00690.02880.00750.0554-53.571434.2845-48.7464
62.963-0.9138-0.01161.59450.81812.55640.02310.3663-0.1684-0.1691-0.02010.03470.0217-0.0556-0.0030.144-0.0346-0.02670.0618-0.02290.0595-49.71625.4117-61.9283
72.2108-0.92280.0442.81820.24992.72480.06380.0954-0.0242-0.14940.1049-0.2148-0.01680.3318-0.16870.2008-0.08250.01940.0817-0.0260.0878-16.2878-26.7819-48.0714
82.6195-0.7678-0.64283.04870.30762.58860.12110.47790.3141-0.7603-0.0035-0.164-0.62720.1899-0.11760.4749-0.13160.06430.17150.06930.0736-19.9841-16.8554-60.4864
92.0284-0.1792-0.40232.11230.39162.7028-0.06760.11370.122-0.12060.1657-0.40640.19920.3347-0.09810.0378-0.00530.03060.0908-0.03880.1486-42.61355.1932-93.5455
101.9996-0.1923-0.56151.4730.35813.1409-0.0764-0.29080.20440.23790.1288-0.2452-0.00710.2906-0.05230.05520.0177-0.05260.0813-0.07660.1353-44.914810.3678-78.2068
113.5008-0.2922-0.23792.29340.47373.0689-0.26690.03030.120.17590.21180.28310.25690.02710.0550.15410.05390.05650.03730.04650.061-45.2672-18.2574-94.9058
124.4810.57510.08331.8191-0.15183.6104-0.285-0.8342-0.16760.79160.15260.13510.67030.14980.13240.57390.21930.12170.2060.06580.0319-42.4688-24.676-80.2097
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A101 - 162
2X-RAY DIFFRACTION1A251 - 275
3X-RAY DIFFRACTION2A163 - 250
4X-RAY DIFFRACTION3B100 - 162
5X-RAY DIFFRACTION3B251 - 275
6X-RAY DIFFRACTION4B163 - 250
7X-RAY DIFFRACTION5C101 - 162
8X-RAY DIFFRACTION5C251 - 276
9X-RAY DIFFRACTION6C163 - 250
10X-RAY DIFFRACTION7D101 - 162
11X-RAY DIFFRACTION7D251 - 275
12X-RAY DIFFRACTION8D163 - 250
13X-RAY DIFFRACTION9E101 - 162
14X-RAY DIFFRACTION9E251 - 275
15X-RAY DIFFRACTION10E163 - 250
16X-RAY DIFFRACTION11F101 - 162
17X-RAY DIFFRACTION11F251 - 275
18X-RAY DIFFRACTION12F163 - 250

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