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- PDB-4d70: Structural, biophysical and biochemical analyses of a Clostridium... -

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Basic information

Entry
Database: PDB / ID: 4d70
TitleStructural, biophysical and biochemical analyses of a Clostridium perfringens Sortase D5 transpeptidase
ComponentsSORTASE FAMILY PROTEIN
KeywordsHYDROLASE
Function / homology
Function and homology information


Sortase D, type 2 / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Sortase family protein / Uncharacterized protein
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsSuryadinata, R. / Seabrook, S. / Adams, T.E. / Nuttall, S.D. / Peat, T.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural and Biochemical Analyses of a Clostridium Perfringens Sortase D Transpeptidase
Authors: Suryadinata, R. / Seabrook, S.A. / Adams, T.E. / Nuttall, S.D. / Peat, T.S.
History
DepositionNov 19, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Dec 20, 2023Group: 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_sheet
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_sheet.number_strands
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SORTASE FAMILY PROTEIN
B: SORTASE FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,8832
Polymers41,8832
Non-polymers00
Water1,71195
1
A: SORTASE FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)20,9421
Polymers20,9421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SORTASE FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)20,9421
Polymers20,9421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.776, 65.582, 68.057
Angle α, β, γ (deg.)90.00, 93.86, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A27 - 186
2010B27 - 186

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Components

#1: Protein SORTASE FAMILY PROTEIN / SORTASE


Mass: 20941.508 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 23-187
Source method: isolated from a genetically manipulated source
Details: THE FIRST 22 AMINO ACIDS WERE REMOVED AND A HIS-TAG WAS ENGINEERED AT THE N-TERMINAL DOMAIN TO AID IN PURIFICATION.
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0TUL5, UniProt: Q8XNW0*PLUS, sortase A
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 22 AMINO ACIDS WERE REMOVED AND REPLACED WITH A N-TERMINAL HIS-TAG.

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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: 2.41 Å3/Da / Density % sol: 48.9 % / Description: NONE
Crystal growTemperature: 281 K / Method: vapor diffusion / pH: 5.5
Details: THE PROTEIN CONCENTRATION WAS 20 MG/ML AND THE RESERVOIR CONDITIONS WERE 0.2M AMMONIUM ACETATE, 25% PEG 3350, 0.1M BIS-TRIS CHLORIDE AT PH 5.5 AND INCUBATED AT 8C.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9191
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9191 Å / Relative weight: 1
ReflectionResolution: 1.99→47.2 Å / Num. obs: 23533 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18
Reflection shellResolution: 1.99→2.09 Å / Redundancy: 7 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3.2 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G66

3g66


Resolution: 1.99→67.9 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 8.059 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21335 1214 5.2 %RANDOM
Rwork0.17569 ---
obs0.17769 22304 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.509 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20.4 Å2
2---0.85 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.99→67.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 0 0 95 2621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192630
X-RAY DIFFRACTIONr_bond_other_d0.0060.022530
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.9563556
X-RAY DIFFRACTIONr_angle_other_deg1.22735860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7455334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.91726.842133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05315509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.386158
X-RAY DIFFRACTIONr_chiral_restr0.110.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023034
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02554
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_it3.5263.8561318
X-RAY DIFFRACTIONr_mcbond_other3.5273.8551317
X-RAY DIFFRACTIONr_mcangle_it4.4746.4551658
X-RAY DIFFRACTIONr_mcangle_other4.4746.4561659
X-RAY DIFFRACTIONr_scbond_it5.164.671312
X-RAY DIFFRACTIONr_scbond_other5.1584.671313
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4377.5061899
X-RAY DIFFRACTIONr_long_range_B_refined8.3316.41611291
X-RAY DIFFRACTIONr_long_range_B_other8.32216.411249
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9552 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.986→2.037 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 83 -
Rwork0.245 1568 -
obs--94.18 %
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)
10.8071-0.06730.35830.678-0.03791.1391-0.04280.20690.0271-0.05820.12660.00240.07080.0043-0.08380.0258-0.0344-0.00580.09180.01520.012715.9715.7717.5421
21.0044-0.31230.28510.7304-0.12330.37090.0442-0.1391-0.02090.0563-0.02940.0418-0.0261-0.0046-0.01480.0192-0.01260.01870.04060.01190.044335.100313.229938.0139
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 186
2X-RAY DIFFRACTION2B27 - 186

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