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Basic information

Entry
Database: PDB / ID: 3tbe
TitleThe crystal structure of the complex of Streptococcus agalactiae sortase C1 and MTSET
ComponentsSortase family protein
KeywordsHYDROLASE / Beta-barrel / Pili-biogenesis / 2-(trimethylammonium)-ethyl-methanethiosulfonate bromide
Function / homology
Function and homology information


hydrolase activity / membrane
Similarity search - Function
Sortase C / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
2-(TRIMETHYLAMMONIUM)ETHYL THIOL / Sortase family protein
Similarity search - Component
Biological speciesStreptococcus agalactiae serogroup V (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsKhare, B.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Crystal Structure Analysis of Group B Streptococcus Sortase C1: A Model for the "Lid" Movement upon Substrate Binding.
Authors: Khare, B. / Fu, Z.Q. / Huang, I.H. / Ton-That, H. / Narayana, S.V.
History
DepositionAug 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Dec 21, 2011Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 14, 2019Group: Data collection / Category: computing
Revision 1.5Sep 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sortase family protein
B: Sortase family protein
C: Sortase family protein
D: Sortase family protein
E: Sortase family protein
F: Sortase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,88918
Polymers154,6516
Non-polymers1,23712
Water1,946108
1
A: Sortase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8952
Polymers25,7751
Non-polymers1201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sortase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0884
Polymers25,7751
Non-polymers3123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sortase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0274
Polymers25,7751
Non-polymers2523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Sortase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9923
Polymers25,7751
Non-polymers2162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Sortase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8952
Polymers25,7751
Non-polymers1201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Sortase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9923
Polymers25,7751
Non-polymers2162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.410, 70.650, 194.440
Angle α, β, γ (deg.)90.00, 90.43, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13E
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A5 - 200
2112B5 - 200
1122C5 - 200
2122D5 - 200
1132E5 - 200
2132F5 - 200

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Sortase family protein / Sortase C1 / Pilus-specific sortase


Mass: 25775.227 Da / Num. of mol.: 6 / Fragment: UNP residues 43-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae serogroup V (bacteria)
Strain: SAG 2603V/R / Gene: SAG0647 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1Blue
References: UniProt: Q8E0S7, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical
ChemComp-ETM / 2-(TRIMETHYLAMMONIUM)ETHYL THIOL


Mass: 120.236 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H14NS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M ammonium sulfate, 5% PEG3350, 0.446 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.85→196.116 Å / Num. all: 39189 / Num. obs: 38964 / % possible obs: 99.6 % / Redundancy: 3.45 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.1
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 3.57 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
PHASERphasing
CNSrefinement
StructureStudiodata collection
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TB7

3tb7


Resolution: 2.85→27.707 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.859 / SU B: 18.486 / SU ML: 0.357 / Cross valid method: THROUGHOUT / ESU R: 2.36 / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29604 1956 5 %RANDOM
Rwork0.25033 ---
obs0.25266 36974 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.923 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20.05 Å2
2---0.14 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.85→27.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8832 0 68 108 9008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0229062
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.96812306
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.02151130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.29923.643398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.865151475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9561566
X-RAY DIFFRACTIONr_chiral_restr0.1020.21439
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216749
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0681.55699
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.01729152
X-RAY DIFFRACTIONr_scbond_it2.07233363
X-RAY DIFFRACTIONr_scangle_it3.7614.53154
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A692TIGHT POSITIONAL0.060.05
1A658MEDIUM POSITIONAL0.070.5
1A692TIGHT THERMAL0.580.5
1A658MEDIUM THERMAL0.652
2C672TIGHT POSITIONAL0.080.05
2C634MEDIUM POSITIONAL0.10.5
2C672TIGHT THERMAL1.20.5
2C634MEDIUM THERMAL1.332
3E676TIGHT POSITIONAL0.050.05
3E635MEDIUM POSITIONAL0.090.5
3E676TIGHT THERMAL0.890.5
3E635MEDIUM THERMAL0.942
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.477 128 -
Rwork0.376 2763 -
obs--99.93 %

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