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- PDB-5txu: 1.95 Angstrom Resolution Crystal Structure of Stage II Sporulatio... -

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Basic information

Entry
Database: PDB / ID: 5txu
Title1.95 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (SpoIID) from Clostridium difficile in Apo Conformation
ComponentsStage II sporulation protein D
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Sporulation stage II protein D, amidase enhancer LytB / Sporulation stage II protein D, amidase enhancer LytB N-terminal / Sporulation stage II, protein D firmicutes / Stage II sporulation protein / :
Similarity search - Domain/homology
FORMIC ACID / Stage II sporulation protein D
Similarity search - Component
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsNocadello, S. / Minasov, G. / Kiryukhina, O. / Shuvalova, L. / 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 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.2Apr 1, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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

Downloads & links

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Assembly

Deposited unit
A: Stage II sporulation protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,33726
Polymers40,0641
Non-polymers1,27425
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-13 kcal/mol
Surface area14220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.043, 98.043, 108.241
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-776-

HOH

21A-789-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Stage II sporulation protein D


Mass: 40063.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile (strain 630) (bacteria)
Strain: 630 / Gene: spoIID, CD630_01240 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q18CL6

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Non-polymers , 6 types, 353 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.75 Å3/Da / Density % sol: 67.19 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 7
Details: Protein: 7.0 mg/ml, 0.5M Sodium chloride, 0.05M Tris-HCl pH=7.2, 1/100 (v/v) Elastase, 2mM CB1. Crystallization condiction: Sodium Malonate 2M, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 5, 2016 / Details: C(111)
RadiationMonochromator: Beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 44267 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 15.37
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 5.1 / CC1/2: 0.98 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I1T

5i1t


Resolution: 1.95→29.06 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.032 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.093 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18397 2094 4.7 %RANDOM
Rwork0.15886 ---
obs0.16005 42138 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.319 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å2-0 Å2
2---0.09 Å20 Å2
3---0.31 Å2
Refinement stepCycle: 1 / Resolution: 1.95→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 72 328 2680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022475
X-RAY DIFFRACTIONr_bond_other_d0.0010.022366
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.9713319
X-RAY DIFFRACTIONr_angle_other_deg0.83335491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3655314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.42425.045111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4915470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.542157
X-RAY DIFFRACTIONr_chiral_restr0.0940.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.022791
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02560
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_it1.4222.3371169
X-RAY DIFFRACTIONr_mcbond_other1.4222.341170
X-RAY DIFFRACTIONr_mcangle_it2.3193.4891467
X-RAY DIFFRACTIONr_mcangle_other2.3183.4891468
X-RAY DIFFRACTIONr_scbond_it2.0562.7491306
X-RAY DIFFRACTIONr_scbond_other2.0552.7521307
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0333.8831838
X-RAY DIFFRACTIONr_long_range_B_refined10.00330.432958
X-RAY DIFFRACTIONr_long_range_B_other9.93328.4122853
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 130 -
Rwork0.188 3097 -
obs--99.57 %
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)
12.1708-1.11930.65262.9329-0.67173.34920.11430.0692-0.0706-0.0679-0.0584-0.39690.31640.3809-0.05580.2767-0.073-0.07850.0930.03220.211563.3493-0.22160.4134
26.33991.54210.98057.6882-1.37119.4667-0.35620.2829-0.2850.1240.1894-0.26750.7945-0.0240.16680.27280.03880.00890.04480.0180.184966.5245-16.21150.372
31.22860.3587-0.31233.0277-0.80784.99190.04870.0419-0.0438-0.1926-0.0467-0.40870.01910.2363-0.00210.1671-0.0617-0.05110.04360.03340.131262.62694.4915-3.9653
41.01660.76180.57171.62740.7931.87590.2014-0.1033-0.15010.1041-0.1602-0.10010.2205-0.2402-0.04120.2439-0.0948-0.03560.08040.06490.131341.0389-10.0809-7.3089
51.52870.97660.95991.75890.76571.38020.1447-0.1688-0.05480.137-0.1083-0.01130.0733-0.2252-0.03640.2222-0.1017-0.03160.09740.06540.108540.8975-6.975-5.03
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A71 - 130
2X-RAY DIFFRACTION2A131 - 137
3X-RAY DIFFRACTION3A138 - 188
4X-RAY DIFFRACTION4A189 - 258
5X-RAY DIFFRACTION5A259 - 354

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