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- PDB-1t2w: Crystal Structure of Sortase A in Complex with a LPETG peptide -

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Basic information

Entry
Database: PDB / ID: 1t2w
TitleCrystal Structure of Sortase A in Complex with a LPETG peptide
Components
  • Class A sortase SrtA
  • Peptide LEU-PRO-GLU-THR-GLY
KeywordsHYDROLASE / Sortase / transpeptidase / BETA BARREL
Function / homology
Function and homology information


calcium-dependent cysteine-type endopeptidase activity / peptide binding / manganese ion binding / calcium ion binding / magnesium ion binding / proteolysis
Similarity search - Function
Sortase A / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZong, Y. / Bice, T.W. / Ton-That, H. / Schneewind, O. / Narayana, S.V.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of Staphylococcus aureus sortase A and its substrate complex
Authors: Zong, Y. / Bice, T.W. / Ton-That, H. / Schneewind, O. / Narayana, S.V.
History
DepositionApr 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 27, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / reflns / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.group_PDB ..._atom_site.auth_asym_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_validate_close_contact.auth_asym_id_2 / _reflns.d_resolution_low / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_name / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Revision 2.1Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Class A sortase SrtA
B: Class A sortase SrtA
C: Class A sortase SrtA
D: Peptide LEU-PRO-GLU-THR-GLY


Theoretical massNumber of molelcules
Total (without water)49,6874
Polymers49,6874
Non-polymers00
Water4,035224
1
A: Class A sortase SrtA
D: Peptide LEU-PRO-GLU-THR-GLY


Theoretical massNumber of molelcules
Total (without water)16,9062
Polymers16,9062
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Class A sortase SrtA


Theoretical massNumber of molelcules
Total (without water)16,3911
Polymers16,3911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Class A sortase SrtA


Theoretical massNumber of molelcules
Total (without water)16,3911
Polymers16,3911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.640, 82.670, 56.290
Angle α, β, γ (deg.)90.00, 103.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Class A sortase SrtA / LPXTG specific sortase A / Sortase / Sortase A / Sortase family protein


Mass: 16390.531 Da / Num. of mol.: 3 / Fragment: Sortase A (residues 62-206) complexed with LPETG / Mutation: C184A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: srtA, srtA_2, A7Q05_0203, A7U51_2758, DD547_02559, DQV53_14585, EP54_00580, EQ90_03180, ER624_01345, ERS365775_01887, FA040_11075, G6Y10_05930, GO814_08865, GZ145_04475, H4Q63_05340, HMPREF2819_ ...Gene: srtA, srtA_2, A7Q05_0203, A7U51_2758, DD547_02559, DQV53_14585, EP54_00580, EQ90_03180, ER624_01345, ERS365775_01887, FA040_11075, G6Y10_05930, GO814_08865, GZ145_04475, H4Q63_05340, HMPREF2819_05680, HMPREF3211_00152, HT539_09110, HW113_13780, HYH24_12580, LG33_14175, NCTC10654_02700, NCTC10988_02942, RK65_002860, SABB_01155, SAHC1340_00378, SAMEA103891215_00596, SAMEA103891286_01213, SAMEA103891321_01196, SAMEA1966928_00247, SAMEA1969845_01250, SAMEA1972827_00954, SAMEA2076218_00454, SAMEA2076226_00491, SAMEA2076235_01010, SAMEA2076464_00854, SAMEA2076470_01152, SAMEA2076472_01070, SAMEA2076475_01144, SAMEA2076481_00167, SAMEA2076758_00629, SAMEA2077031_00874, SAMEA2077046_00836, SAMEA2077832_00359, SAMEA2078252_01155, SAMEA2078307_01069, SAMEA2078308_00562, SAMEA2078558_00738, SAMEA2078569_01198, SAMEA2078588_01162, SAMEA2078824_00854, SAMEA2078837_00966, SAMEA2079048_01261, SAMEA2079512_01291, SAMEA2079517_02158, SAMEA2079727_00616, SAMEA2079728_00978, SAMEA2079949_00908, SAMEA2079951_00489, SAMEA2079957_00669, SAMEA2079958_00786, SAMEA2079968_00740, SAMEA2080812_00148, SAMEA2080900_00941, SAMEA2080904_01047, SAMEA2080913_01192, SAMEA2081043_00247, SAMEA2081054_00932, SAMEA2081211_00203, SAMEA2081362_00521, SAMEA2081458_00784, SAMEA2081475_00930, SAMEA4008573_00649, SAMEA4008676_00205, SAMEA958779_01435, SAMEA958793_00205, SAMEA958804_00204, SAMEA958836_00599, SAMEA958838_01748, SAMEA958987_01810
Plasmid: Novagen pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue / References: UniProt: Q9S446
#2: Protein/peptide Peptide LEU-PRO-GLU-THR-GLY


Mass: 515.557 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
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: 1.9 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.35
Details: Ammonium Sulfate, MES, Sodium Chloride, pH 6.35, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 5, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9979 Å / Relative weight: 1
ReflectionResolution: 1.8→27.31 Å / Num. all: 37608 / Num. obs: 34240 / % possible obs: 91.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 11 Å2
Reflection shellResolution: 1.8→1.9 Å / % possible all: 91.2

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T2O

1t2o


Resolution: 1.8→27.31 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 766432.57 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2805 10 %RANDOM
Rwork0.186 ---
all0.195 37680 --
obs0.186 34240 74.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.0958 Å2 / ksol: 0.408279 e/Å3
Displacement parametersBiso mean: 34 Å2
Baniso -1Baniso -2Baniso -3
1-4.74 Å20 Å2-1.53 Å2
2---4.55 Å20 Å2
3----0.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å0.02 Å
Refinement stepCycle: LAST / Resolution: 1.8→27.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 0 36 224 3622
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.035
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d1.23
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.22 280 10.1 %
Rwork0.174 2506 -
obs--44.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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