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- PDB-5jcv: Sortase B from Listeria monocytogenes. -

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Basic information

Entry
Database: PDB / ID: 5jcv
TitleSortase B from Listeria monocytogenes.
ComponentsLmo2181 protein
KeywordsHYDROLASE / sortase / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


cellular response to iron ion / membrane => GO:0016020 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / hydrolase activity / plasma 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
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.23 Å
AuthorsOsipiuk, J. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200700058C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: to be published
Title: Sortase B from Listeria monocytogenes.
Authors: Osipiuk, J. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lmo2181 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8863
Polymers21,7551
Non-polymers1322
Water39622
1
A: Lmo2181 protein
hetero molecules

A: Lmo2181 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7726
Polymers43,5092
Non-polymers2634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area1860 Å2
ΔGint-47 kcal/mol
Surface area18260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.155, 70.155, 224.471
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Lmo2181 protein


Mass: 21754.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: lmo2181 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Y588
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.32 Å3/Da / Density % sol: 62.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M lithium sulfate, 2 M ammonium sulfate, 0.1 M Tris-Cl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2015
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.23→33.6 Å / Num. obs: 14055 / % possible obs: 99.2 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.087 / Net I/av σ(I): 11.1 / Net I/σ(I): 36.4
Reflection shellResolution: 2.23→2.27 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.88 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
REFMAC5.8.0069refinement
PHENIX1.9-1692refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.23→33.6 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 13.423 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.189
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 683 4.9 %RANDOM
Rwork0.2066 ---
obs0.2087 13369 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 142.57 Å2 / Biso mean: 65.891 Å2 / Biso min: 37.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å20 Å2
2--0.21 Å2-0 Å2
3----0.41 Å2
Refinement stepCycle: final / Resolution: 2.23→33.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 6 22 1480
Biso mean--94.59 52.11 -
Num. residues----175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021498
X-RAY DIFFRACTIONr_bond_other_d0.0010.021383
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9642026
X-RAY DIFFRACTIONr_angle_other_deg0.79533193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0145177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77524.93779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2115260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.264156
X-RAY DIFFRACTIONr_chiral_restr0.0990.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021683
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02351
X-RAY DIFFRACTIONr_mcbond_it3.1784.309702
X-RAY DIFFRACTIONr_mcbond_other3.1774.307701
X-RAY DIFFRACTIONr_mcangle_it4.6456.439875
LS refinement shellResolution: 2.233→2.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 45 -
Rwork0.285 958 -
all-1003 -
obs--98.72 %
Refinement TLS params.Method: refined / Origin x: 17.2656 Å / Origin y: -1.8639 Å / Origin z: 67.2407 Å
111213212223313233
T0.0701 Å2-0.0855 Å20.0174 Å2-0.4001 Å2-0.0752 Å2--0.055 Å2
L0.5364 °20.0243 °20.221 °2-1.3363 °20.4876 °2--2.3883 °2
S-0.1051 Å °0.2127 Å °-0.0281 Å °-0.0597 Å °0.2936 Å °0.1203 Å °0.0396 Å °0.5836 Å °-0.1886 Å °

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