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- PDB-4ux7: Structure of a Clostridium difficile sortase -

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Basic information

Entry
Database: PDB / ID: 4ux7
TitleStructure of a Clostridium difficile sortase
ComponentsPUTATIVE PEPTIDASE C60B, SORTASE B
KeywordsHYDROLASE / SORTASE
Function / homology
Function and homology information


hydrolase activity / membrane
Similarity search - Function
Sortase B family / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Peptidase C60B, sortase B
Similarity search - Component
Biological speciesCLOSTRIDIUM DIFFICILE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsChambers, C.J. / Roberts, A.K. / Shone, C.C. / Acharya, K.R.
CitationJournal: Sci.Rep. / Year: 2015
Title: Structure and Function of a Clostridium Difficile Sortase Enzyme.
Authors: Chambers, C.J. / Roberts, A.K. / Shone, C.C. / Acharya, K.R.
History
DepositionAug 19, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUTATIVE PEPTIDASE C60B, SORTASE B
B: PUTATIVE PEPTIDASE C60B, SORTASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4367
Polymers56,6412
Non-polymers7955
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint0.1 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.247, 90.273, 134.738
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PUTATIVE PEPTIDASE C60B, SORTASE B / SORTASE B


Mass: 28320.658 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM DIFFICILE (bacteria) / Strain: 630 / Description: SYNTHETIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q183F3, sortase B
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL POLYHISTIDINE TAG, C116A MUTATION

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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: 2.06 Å3/Da / Density % sol: 40.23 % / Description: NONE
Crystal growpH: 4.2 / Details: 0.1M PHOSPHATE-CITRATE PH 4.2, 40% PEG 300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.55→29.37 Å / Num. obs: 15902 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.8
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SWISS-MODELLER MODEL BASED ON PDB ENTRY 1RZ2

1rz2


Resolution: 2.55→75 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.869 / SU B: 10.674 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.922 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26221 793 5 %RANDOM
Rwork0.19623 ---
obs0.19948 15039 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.962 Å2
Baniso -1Baniso -2Baniso -3
1--2.97 Å20 Å20 Å2
2--5.74 Å20 Å2
3----2.76 Å2
Refinement stepCycle: LAST / Resolution: 2.55→75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3377 0 50 66 3493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023492
X-RAY DIFFRACTIONr_bond_other_d0.0020.023300
X-RAY DIFFRACTIONr_angle_refined_deg1.241.9544674
X-RAY DIFFRACTIONr_angle_other_deg0.7637640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0075406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33125.682176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.59815658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.964156
X-RAY DIFFRACTIONr_chiral_restr0.0750.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023884
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02810
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_it1.5332.8661630
X-RAY DIFFRACTIONr_mcbond_other1.5282.8641629
X-RAY DIFFRACTIONr_mcangle_it2.6754.2942034
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5573.0761862
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 55 -
Rwork0.268 1061 -
obs--99.91 %

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