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- PDB-5a0d: N-terminal thioester domain of surface protein from Clostridium p... -

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Basic information

Entry
Database: PDB / ID: 5a0d
TitleN-terminal thioester domain of surface protein from Clostridium perfringens, Cys138Ala mutant
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 / SAD / Resolution: 1.6 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 17, 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,82911
Polymers84,3954
Non-polymers4347
Water6,702372
1
A: SURFACE ANCHORED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2233
Polymers21,0991
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SURFACE ANCHORED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2854
Polymers21,0991
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SURFACE ANCHORED PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,0991
Polymers21,0991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SURFACE ANCHORED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2233
Polymers21,0991
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.420, 110.720, 68.770
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
SURFACE ANCHORED PROTEIN


Mass: 21098.752 Da / Num. of mol.: 4 / Fragment: THIOESTER DOMAIN, UNP RESIDUES 92-277 / Mutation: YES
Source method: isolated from a genetically manipulated source
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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCYS138ALA MUTATION IN THIS STRUCTURE

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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: 2.23 Å3/Da / Density % sol: 44.8 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2 M POTASSIUM THIOCYANATE, 0.1 M BIS -TRIS PROPANE PH 6.5, 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: Sep 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→44.97 Å / Num. obs: 99659 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 18.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 31.6
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 18.1 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 4.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.6→44.97 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.056 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21015 4972 5 %RANDOM
Rwork0.17747 ---
obs0.17906 94622 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.329 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.6→44.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5565 0 28 372 5965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026454
X-RAY DIFFRACTIONr_bond_other_d0.0010.026153
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9718733
X-RAY DIFFRACTIONr_angle_other_deg0.787314134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9015792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1725.347303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.725151122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3111524
X-RAY DIFFRACTIONr_chiral_restr0.090.2982
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027323
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021461
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_it1.0891.5213174
X-RAY DIFFRACTIONr_mcbond_other1.0891.5213173
X-RAY DIFFRACTIONr_mcangle_it1.6592.2793964
X-RAY DIFFRACTIONr_mcangle_other1.6582.283965
X-RAY DIFFRACTIONr_scbond_it1.8511.6923280
X-RAY DIFFRACTIONr_scbond_other1.8491.6923280
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.682.4684770
X-RAY DIFFRACTIONr_long_range_B_refined4.42312.4066596
X-RAY DIFFRACTIONr_long_range_B_other4.42312.4096597
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 392 -
Rwork0.205 6864 -
obs--99.89 %
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)
10.7519-0.18120.02461.1245-0.29061.7628-0.019-0.17410.14050.2425-0.0922-0.119-0.1513-0.0710.11110.0871-0.017-0.0320.0659-0.03660.068829.82412.027621.2121
21.4467-0.3872-0.26561.93170.34773.01-0.0511-0.13120.00480.2769-0.05850.09870.4374-0.54280.10960.0986-0.08960.03230.1289-0.03030.018119.6018-10.184122.9779
32.2803-0.54990.13961.27280.3030.9560.0286-0.1381-0.08880.12410.0314-0.0210.09490.0544-0.060.02450.00770.00290.01880.01340.032247.065519.06158.2541
42.9109-0.28350.60581.43830.27290.9285-0.0071-0.20070.27150.0291-0.06240.0364-0.0685-0.07770.06950.0164-0.00180.01710.0196-0.02690.063538.47832.8359.5177
52.0704-0.2078-0.9241.0854-0.6322.57240.06430.2511-0.1205-0.20040.01760.06230.1217-0.1329-0.08190.05220.0173-0.00640.0994-0.01640.022645.431619.5888-20.6803
63.1072-1.14220.83021.4469-0.36931.47610.02890.18760.2166-0.0994-0.0266-0.1397-0.10510.1658-0.00230.0337-0.01350.02070.08340.00210.025755.714630.9446-23.4161
70.98560.18580.34161.31720.25480.8377-0.04660.08680.0434-0.1471-0.0034-0.05560.03310.06580.04990.04480.0104-0.00210.01370.00560.056730.16770.2683-7.4576
81.1986-0.2757-0.12681.29460.27020.8527-0.07570.05260.1895-0.1095-0.02810.1055-0.0304-0.15270.10380.02760.0006-0.05230.0287-0.01020.116715.76947.2192-9.2905
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A102 - 162
2X-RAY DIFFRACTION1A251 - 276
3X-RAY DIFFRACTION2A163 - 250
4X-RAY DIFFRACTION3B101 - 162
5X-RAY DIFFRACTION3B251 - 276
6X-RAY DIFFRACTION4B163 - 250
7X-RAY DIFFRACTION5C102 - 162
8X-RAY DIFFRACTION5C251 - 275
9X-RAY DIFFRACTION6C163 - 250
10X-RAY DIFFRACTION7D102 - 162
11X-RAY DIFFRACTION7D251 - 275
12X-RAY DIFFRACTION8D163 - 250

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