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- PDB-2oqw: The crystal structure of sortase B from B.anthracis in complex wi... -

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Basic information

Entry
Database: PDB / ID: 2oqw
TitleThe crystal structure of sortase B from B.anthracis in complex with AAEK1
ComponentsSortase B
KeywordsHYDROLASE / SortaseB protein / inhibitor / B. anthracis / the Great Lakes Regional Center of Excellence / GLRCE
Function / homology
Function and homology information


hydrolase activity / membrane
Similarity search - Function
Sortase B, Firmicutes / Sortase B family / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
SrtB family sortase / SrtB family sortase
Similarity search - Component
Biological speciesBacillus anthracis str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsWu, R. / Zhang, R. / Marresso, A.W. / Schneewind, O. / Joachimiak, A.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Activation of inhibitors by sortase triggers irreversible modification of the active site.
Authors: Maresso, A.W. / Wu, R. / Kern, J.W. / Zhang, R. / Janik, D. / Missiakas, D.M. / Duban, M.E. / Joachimiak, A. / Schneewind, O.
History
DepositionFeb 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sortase B


Theoretical massNumber of molelcules
Total (without water)26,9291
Polymers26,9291
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.436, 73.806, 89.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthis protein exists as a monomer

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Components

#1: Protein Sortase B / Hypothetical protein


Mass: 26928.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. (bacteria) / Strain: Ames / Gene: BA_4783, BAS4438, GBAA4783 / Plasmid: pDM68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q81L49, UniProt: A0A6L8PZR0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE E.C. NUMBER FOR THIS PROTEIN IS 3.4.22.B51 ACCORDING TO BRENDA ENZYME INFORMATION SYSTEM.

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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: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M MgCl2, 25% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2006 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 14492 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 20.95
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.87 / Num. unique all: 1119 / % possible all: 72.33

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→44.54 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.945 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.211
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25871 691 5.1 %RANDOM
Rwork0.18677 ---
all0.19038 12870 --
obs0.19038 12870 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.175 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---2.11 Å20 Å2
3---2.08 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1753 0 0 85 1838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221793
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.9562408
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5965208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36724.58396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.4915335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.331510
X-RAY DIFFRACTIONr_chiral_restr0.1510.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021356
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.2730
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21211
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.294
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0011.51072
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55121685
X-RAY DIFFRACTIONr_scbond_it2.3013828
X-RAY DIFFRACTIONr_scangle_it3.3984.5723
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 50 -
Rwork0.189 773 -
obs-823 80.37 %
Refinement TLS params.Method: refined / Origin x: 13.9762 Å / Origin y: 5.4348 Å / Origin z: 11.7745 Å
111213212223313233
T-0.1023 Å20.0105 Å2-0.0042 Å2--0.0673 Å20.0207 Å2---0.0714 Å2
L1.4457 °20.1277 °20.2423 °2-3.3252 °2-0.1392 °2--1.3987 °2
S0.0579 Å °0.0287 Å °-0.052 Å °0.0064 Å °0.0292 Å °0.0438 Å °0.0724 Å °-0.0116 Å °-0.0871 Å °

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