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- PDB-5tta: A 1.85A X-Ray Structure from Peptoclostridium difficile 630 of a ... -

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Basic information

Entry
Database: PDB / ID: 5tta
TitleA 1.85A X-Ray Structure from Peptoclostridium difficile 630 of a Hypothetical Protein
ComponentsPutative exported protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Alpha/Beta protein / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyDomain of unknown function DUF5780 / Family of unknown function (DUF5780) / Exported protein
Function and homology information
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsBrunzelle, J.S. / Minasov, G. / Shuvalova, L. / Cordona-Correa, A. / Dubrovska, I. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2023
Title: A high-throughput structural system biology approach to increase structure representation of proteins from Clostridioides difficile.
Authors: Rosas-Lemus, M. / Dey, S. / Minasov, G. / Tan, K. / Anderson, S.M. / Brunzelle, J. / Nocadello, S. / Shabalin, I. / Filippova, E. / Halavaty, A. / Kim, Y. / Maltseva, N. / Osipiuk, J. / ...Authors: Rosas-Lemus, M. / Dey, S. / Minasov, G. / Tan, K. / Anderson, S.M. / Brunzelle, J. / Nocadello, S. / Shabalin, I. / Filippova, E. / Halavaty, A. / Kim, Y. / Maltseva, N. / Osipiuk, J. / Minor, W. / Joachimiak, A. / Savchenko, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionNov 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 18, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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: Putative exported protein
B: Putative exported protein


Theoretical massNumber of molelcules
Total (without water)56,5622
Polymers56,5622
Non-polymers00
Water5,891327
1
A: Putative exported protein

B: Putative exported protein


Theoretical massNumber of molelcules
Total (without water)56,5622
Polymers56,5622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area1410 Å2
ΔGint-14 kcal/mol
Surface area23410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.780, 51.040, 81.120
Angle α, β, γ (deg.)73.38, 82.06, 86.35
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Putative exported protein


Mass: 28280.869 Da / Num. of mol.: 2 / Fragment: UNP residues 30-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile (bacteria) / Strain: 630 / Gene: CD630_21270 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q185R5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 14.5mg/ml, 0.1M Tris HCl (pH 8.3) Screen: PACT (A3), 0.1M SPG buffer (pH 6.0), 25% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 19, 2015 / Details: KB Bi-morph Mirrors
RadiationMonochromator: Double Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.85→30.475 Å / Num. obs: 39052 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 25.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Net I/σ(I): 18.7
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 3.3 / CC1/2: 0.921 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIXdev_2203refinement
XDSautoPROCdata reduction
AimlessautoPROCdata scaling
PHENIXdev_2203phasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→30.475 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.29
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 1891 5.33 %Random
Rwork0.1797 ---
obs0.1824 35459 88.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→30.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 0 327 3761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083539
X-RAY DIFFRACTIONf_angle_d0.8064803
X-RAY DIFFRACTIONf_dihedral_angle_d14.1992091
X-RAY DIFFRACTIONf_chiral_restr0.059489
X-RAY DIFFRACTIONf_plane_restr0.006620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8501-1.89630.3026580.30021402X-RAY DIFFRACTION51
1.8963-1.94760.3061930.24111648X-RAY DIFFRACTION62
1.9476-2.00490.3181110.23651907X-RAY DIFFRACTION70
2.0049-2.06960.29721300.222236X-RAY DIFFRACTION82
2.0696-2.14350.25141600.21662451X-RAY DIFFRACTION92
2.1435-2.22930.281420.20792664X-RAY DIFFRACTION97
2.2293-2.33080.23981620.20682611X-RAY DIFFRACTION98
2.3308-2.45360.25731430.20052645X-RAY DIFFRACTION98
2.4536-2.60720.26011600.20592629X-RAY DIFFRACTION98
2.6072-2.80840.2521490.2052678X-RAY DIFFRACTION98
2.8084-3.09080.23971420.19332691X-RAY DIFFRACTION99
3.0908-3.53750.24061550.17542628X-RAY DIFFRACTION99
3.5375-4.45460.20491380.14412722X-RAY DIFFRACTION99
4.4546-30.47920.16371480.14032656X-RAY DIFFRACTION98

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