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- PDB-9blp: T450S mutant of repeat domain 2 from Clostridium perfringens adhe... -

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Basic information

Entry
Database: PDB / ID: 9blp
TitleT450S mutant of repeat domain 2 from Clostridium perfringens adhesin CPE0147 with intramolecular ester bond
ComponentsSurface anchored protein
KeywordsUNKNOWN FUNCTION / repeat domain / adhesin / bacterial adhesion / Ig-like domain
Function / homology
Function and homology information


metal ion binding / membrane
Similarity search - Function
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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Putative surface anchored protein
Similarity search - Component
Biological speciesClostridium perfringens B str. ATCC 3626 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSquire, C.J. / Yosaatmadja, Y.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Marsden Fund New Zealand
CitationJournal: Protein Sci. / Year: 2025
Title: Protease mimicry: Dissecting the ester bond crosslinking mechanics in bacterial adhesin proteins.
Authors: Yosaatmadja, Y. / Ung, V. / Liu, X. / Zhao, Y. / Wardega, J.K. / Shetty, A. / Schoensee, S. / Leung, I.K.H. / Keown, J.R. / Goldstone, D.C. / Baker, E.N. / Young, P.G. / Mercadante, D. / Squire, C.J.
History
DepositionMay 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2025Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Surface anchored protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1294
Polymers16,9871
Non-polymers1423
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.907, 44.166, 64.704
Angle α, β, γ (deg.)90.000, 110.107, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Surface anchored protein


Mass: 16986.559 Da / Num. of mol.: 1 / Fragment: Repeat domain 2, residues 439-587 / Mutation: T450S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens B str. ATCC 3626 (bacteria)
Gene: AC1_0147 / Plasmid: pPROEXHTa / Production host: Escherichia coli (E. coli) / References: UniProt: B1R775
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium thiocyanate and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.2→17.86 Å / Num. obs: 44396 / % possible obs: 97.7 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rpim(I) all: 0.018 / Net I/σ(I): 20.2
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2119 / CC1/2: 0.947 / Rpim(I) all: 0.186 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→17.86 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.068 / SU ML: 0.022 / Cross valid method: FREE R-VALUE / ESU R: 0.038 / ESU R Free: 0.036
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1584 2117 4.769 %random selection
Rwork0.142 42278 --
all0.143 ---
obs-44395 97.449 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.799 Å2
Baniso -1Baniso -2Baniso -3
1-0.042 Å20 Å20.018 Å2
2---0.019 Å20 Å2
3----0.029 Å2
Refinement stepCycle: LAST / Resolution: 1.2→17.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1072 0 6 197 1275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131241
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161166
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.6431707
X-RAY DIFFRACTIONr_angle_other_deg1.4031.5952710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8925181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.76127.74262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.48815220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.984151
X-RAY DIFFRACTIONr_chiral_restr0.0630.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021516
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02258
X-RAY DIFFRACTIONr_nbd_refined0.2810.2225
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.21068
X-RAY DIFFRACTIONr_nbtor_refined0.150.2557
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2568
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2124
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.160.24
X-RAY DIFFRACTIONr_nbd_other0.1860.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0980.217
X-RAY DIFFRACTIONr_mcbond_it0.7041.205639
X-RAY DIFFRACTIONr_mcbond_other0.7021.205638
X-RAY DIFFRACTIONr_mcangle_it1.0141.818812
X-RAY DIFFRACTIONr_mcangle_other1.0131.818813
X-RAY DIFFRACTIONr_scbond_it1.0751.435602
X-RAY DIFFRACTIONr_scbond_other1.081.437603
X-RAY DIFFRACTIONr_scangle_it1.3932.064882
X-RAY DIFFRACTIONr_scangle_other1.3922.065883
X-RAY DIFFRACTIONr_lrange_it2.36216.4821362
X-RAY DIFFRACTIONr_lrange_other1.94515.3631305
X-RAY DIFFRACTIONr_rigid_bond_restr0.71932407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.2310.2211590.1882975X-RAY DIFFRACTION94.1707
1.231-1.2650.2161440.1693003X-RAY DIFFRACTION95.7117
1.265-1.3020.1781430.1582928X-RAY DIFFRACTION96.0588
1.302-1.3420.1731370.1352807X-RAY DIFFRACTION96.3036
1.342-1.3860.171360.1322761X-RAY DIFFRACTION96.7279
1.386-1.4340.1511400.1172677X-RAY DIFFRACTION97.1379
1.434-1.4880.1411230.1122573X-RAY DIFFRACTION97.1532
1.488-1.5490.1561390.1142500X-RAY DIFFRACTION97.8495
1.549-1.6180.1491350.1172405X-RAY DIFFRACTION97.9183
1.618-1.6970.1341120.1232313X-RAY DIFFRACTION98.2577
1.697-1.7880.1431100.1212204X-RAY DIFFRACTION98.51
1.788-1.8970.1551280.1272073X-RAY DIFFRACTION98.9213
1.897-2.0280.1331080.1271980X-RAY DIFFRACTION99.0982
2.028-2.190.146870.1331853X-RAY DIFFRACTION99.182
2.19-2.3990.163810.1341709X-RAY DIFFRACTION99.5551
2.399-2.6810.162670.151562X-RAY DIFFRACTION99.694
2.681-3.0950.194600.1521381X-RAY DIFFRACTION99.8614
3.095-3.7880.156540.1431168X-RAY DIFFRACTION99.5925
3.788-5.3470.118340.165908X-RAY DIFFRACTION97.4147
5.347-17.860.255200.241498X-RAY DIFFRACTION93.8406

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