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- PDB-5i1t: 2.6 Angstrom Resolution Crystal Structure of Stage II Sporulation... -

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Basic information

Entry
Database: PDB / ID: 5i1t
Title2.6 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (SpoIID) from Clostridium difficile in Complex with Triacetylchitotriose
ComponentsStage II sporulation protein D
KeywordsHYDROLASE / SpoIID / Triacetylchitotriose / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologySporulation 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 / sporulation resulting in formation of a cellular spore / metal ion binding / triacetyl-beta-chitotriose / Stage II sporulation protein D
Function and homology information
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNocadello, S. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Crystal Structures of the SpoIID Lytic Transglycosylases Essential for Bacterial Sporulation.
Authors: Nocadello, S. / Minasov, G. / Shuvalova, L.S. / Dubrovska, I. / Sabini, E. / Anderson, W.F.
History
DepositionFeb 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.journal_id_CSD / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _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.ptnr2_label_asym_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 / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)38,9177
Polymers37,4461
Non-polymers1,4716
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.082, 98.082, 108.327
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein Stage II sporulation protein D


Mass: 37446.250 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
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 151 molecules

#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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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: 4.05 Å3/Da / Density % sol: 69.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: Protein: 7.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 7.2), 2mM NAG3, 1/100 Elostase; Screen: JCSG+ (B11), 1.6M tri-Sodium citrate pH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 10, 2014 / Details: C(111)
RadiationMonochromator: Beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 18969 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Biso Wilson estimate: 69.1 Å2 / CC1/2: 0.903 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 30.8
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB-4RWR

4rwr


Resolution: 2.6→29.08 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 11.413 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.196 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19629 976 5.2 %RANDOM
Rwork0.15461 ---
obs0.15671 17967 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 69.176 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å2-0.46 Å20 Å2
2---0.92 Å20 Å2
3---2.97 Å2
Refinement stepCycle: 1 / Resolution: 2.6→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 95 147 2522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022466
X-RAY DIFFRACTIONr_bond_other_d0.0010.022318
X-RAY DIFFRACTIONr_angle_refined_deg1.4772.0013325
X-RAY DIFFRACTIONr_angle_other_deg0.8533.0015390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9395292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64425104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.44615449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.809156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.022704
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02538
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_it2.4164.4091159
X-RAY DIFFRACTIONr_mcbond_other2.4164.4091158
X-RAY DIFFRACTIONr_mcangle_it3.616.6141454
X-RAY DIFFRACTIONr_mcangle_other3.6086.6141455
X-RAY DIFFRACTIONr_scbond_it4.2715.2141307
X-RAY DIFFRACTIONr_scbond_other4.2245.2151307
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7017.6271872
X-RAY DIFFRACTIONr_long_range_B_refined8.78136.6962781
X-RAY DIFFRACTIONr_long_range_B_other8.72936.3352743
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.601→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 77 -
Rwork0.2 1285 -
obs--99.71 %
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)
13.4963-0.765-0.21891.972-0.91812.94820.08240.11310.16170.15320.06090.4837-0.4217-0.5344-0.14330.3635-0.03030.1140.1539-0.04030.2-62.59662.6717-0.5129
22.45050.6188-1.0252.2738-0.07363.36060.18280.03730.06740.1731-0.11270.2021-0.1932-0.0913-0.07010.2651-0.05950.06780.0403-0.04580.0672-53.9281-1.81550.422
31.37080.364-0.21394.17580.09630.66630.1425-0.0540.1815-0.1339-0.09210.1195-0.17840.252-0.05040.2305-0.10550.05210.1301-0.0490.0606-36.38116.1037-13.1754
41.83991.1316-1.28241.6588-1.10521.75180.1474-0.17580.01650.1535-0.15960.0355-0.06330.26430.01230.3357-0.10760.04060.1387-0.06580.0548-43.48081.0318-3.2395
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A70 - 152
2X-RAY DIFFRACTION2A153 - 221
3X-RAY DIFFRACTION3A222 - 290
4X-RAY DIFFRACTION4A291 - 354

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