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- PDB-9blo: T450C mutant of repeat domain 2 from Clostridium perfringens adhe... -

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Basic information

Entry
Database: PDB / ID: 9blo
TitleT450C mutant of repeat domain 2 from Clostridium perfringens adhesin CPE0147 without 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: 1.35 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

Downloads & links

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Assembly

Deposited unit
A: Surface anchored protein
B: Surface anchored protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1346
Polymers34,0052
Non-polymers1294
Water5,098283
1
A: Surface anchored protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0673
Polymers17,0031
Non-polymers642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Surface anchored protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0673
Polymers17,0031
Non-polymers642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.983, 44.405, 50.102
Angle α, β, γ (deg.)95.135, 109.360, 110.122
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Surface anchored protein


Mass: 17002.623 Da / Num. of mol.: 2 / Fragment: Repeat domain 2, residues 439-587 / Mutation: T450C
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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.: 283 / 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: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M MgCl2, 0.1 M Tris.HCl pH 8.5, and 30% (w/v) PEG 4000

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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 EIGER X 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: 1.35→18.85 Å / Num. obs: 61888 / % possible obs: 94.8 % / Redundancy: 6.7 % / CC1/2: 1 / Rpim(I) all: 0.023 / Net I/σ(I): 27.8
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2494 / CC1/2: 0.787 / Rpim(I) all: 0.352 / % possible all: 77.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→18.85 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.839 / SU ML: 0.051 / Cross valid method: FREE R-VALUE / ESU R: 0.074 / ESU R Free: 0.068
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2286 3086 5.002 %
Rwork0.1929 58614 -
all0.195 --
obs-61700 94.535 %
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: 15.084 Å2
Baniso -1Baniso -2Baniso -3
1-0.003 Å2-0.026 Å2-0.041 Å2
2--0.04 Å20.026 Å2
3----0.015 Å2
Refinement stepCycle: LAST / Resolution: 1.35→18.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2146 0 4 283 2433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132410
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162225
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.6463280
X-RAY DIFFRACTIONr_angle_other_deg1.2671.5975176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7065338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.52627.719114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55215425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.831151
X-RAY DIFFRACTIONr_chiral_restr0.0440.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022886
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02496
X-RAY DIFFRACTIONr_nbd_refined0.2230.2370
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.21999
X-RAY DIFFRACTIONr_nbtor_refined0.1420.21078
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0680.21106
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2205
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2480.215
X-RAY DIFFRACTIONr_nbd_other0.2180.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.223
X-RAY DIFFRACTIONr_mcbond_it0.8111.4271248
X-RAY DIFFRACTIONr_mcbond_other0.7981.4261243
X-RAY DIFFRACTIONr_mcangle_it1.1092.1441573
X-RAY DIFFRACTIONr_mcangle_other1.112.1441574
X-RAY DIFFRACTIONr_scbond_it0.9531.6251162
X-RAY DIFFRACTIONr_scbond_other0.9511.6241161
X-RAY DIFFRACTIONr_scangle_it1.2212.3571689
X-RAY DIFFRACTIONr_scangle_other1.2212.3581690
X-RAY DIFFRACTIONr_lrange_it2.09718.1062507
X-RAY DIFFRACTIONr_lrange_other1.92417.6942461
X-RAY DIFFRACTIONr_rigid_bond_restr0.54134635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.3850.3422090.3143770X-RAY DIFFRACTION82.1429
1.385-1.4230.2912070.2634199X-RAY DIFFRACTION93.5854
1.423-1.4640.2782010.2694043X-RAY DIFFRACTION93.2747
1.464-1.5090.3232020.3123981X-RAY DIFFRACTION93.7892
1.509-1.5590.3111930.2543845X-RAY DIFFRACTION94.3238
1.559-1.6130.2121990.1683743X-RAY DIFFRACTION94.7596
1.613-1.6740.2131920.1583645X-RAY DIFFRACTION95.2109
1.674-1.7420.2421850.1593506X-RAY DIFFRACTION95.5475
1.742-1.820.21830.153379X-RAY DIFFRACTION95.6755
1.82-1.9080.2241570.1873172X-RAY DIFFRACTION94.547
1.908-2.0110.3021710.2383062X-RAY DIFFRACTION95.4814
2.011-2.1330.2051720.1832903X-RAY DIFFRACTION96.7285
2.133-2.280.2551360.2352762X-RAY DIFFRACTION96.5678
2.28-2.4620.2021400.1692577X-RAY DIFFRACTION96.7937
2.462-2.6970.1961200.1672390X-RAY DIFFRACTION98.0086
2.697-3.0140.2031230.1742152X-RAY DIFFRACTION98.2721
3.014-3.4770.2041070.1691920X-RAY DIFFRACTION98.3981
3.477-4.2530.201840.1691610X-RAY DIFFRACTION98.374
4.253-5.9890.218740.1771261X-RAY DIFFRACTION99.2565
5.989-18.850.226310.19694X-RAY DIFFRACTION96.6667

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