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- PDB-5lhk: Bottromycin maturation enzyme BotP in complex with Mn -

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Basic information

Entry
Database: PDB / ID: 5lhk
TitleBottromycin maturation enzyme BotP in complex with Mn
ComponentsLeucine aminopeptidase 2, chloroplastic
KeywordsHYDROLASE / BotP / Bottromycin / RiPPs / peptidase
Function / homology
Function and homology information


metalloaminopeptidase activity / manganese ion binding / proteolysis / cytoplasm
Similarity search - Function
Peptidase M17, leucyl aminopeptidase, N-terminal / Cytosol aminopeptidase family, N-terminal domain / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Zn peptidases / Aminopeptidase / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BICARBONATE ION / : / BotP
Similarity search - Component
Biological speciesStreptomyces sp. BC16019 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.32 Å
AuthorsKoehnke, J. / Adam, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationKO4116/3-1 Germany
CitationJournal: Chembiochem / Year: 2016
Title: Structure and Substrate Recognition of the Bottromycin Maturation Enzyme BotP.
Authors: Mann, G. / Huo, L. / Adam, S. / Nardone, B. / Vendome, J. / Westwood, N.J. / Muller, R. / Koehnke, J.
History
DepositionJul 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 2.0May 8, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine aminopeptidase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8674
Polymers51,6961
Non-polymers1713
Water5,945330
1
A: Leucine aminopeptidase 2, chloroplastic
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)311,20224
Polymers310,1766
Non-polymers1,02518
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area24650 Å2
ΔGint-134 kcal/mol
Surface area89990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.510, 151.510, 101.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-707-

HOH

21A-931-

HOH

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Components

#1: Protein Leucine aminopeptidase 2, chloroplastic


Mass: 51696.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. BC16019 (bacteria) / Gene: botP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: K4MHW2, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases, leucyl aminopeptidase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 3.24 Å3/Da / Density % sol: 62.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 4000 (10 % w/v)), MES pH 6.5 (0.1 M)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.89 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.89 Å / Relative weight: 1
ReflectionResolution: 2.32→47.21 Å / Num. obs: 30149 / % possible obs: 100 % / Redundancy: 37.8 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 26.8
Reflection shellResolution: 2.32→2.38 Å / Redundancy: 35.7 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 5.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.32→47.21 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.06 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R Free: 0.16 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18977 1466 4.9 %RANDOM
Rwork0.14678 ---
obs0.14891 28658 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.514 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å2-0.42 Å20 Å2
2---0.85 Å20 Å2
3---2.75 Å2
Refinement stepCycle: 1 / Resolution: 2.32→47.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 6 330 3640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193364
X-RAY DIFFRACTIONr_bond_other_d0.0020.023261
X-RAY DIFFRACTIONr_angle_refined_deg1.261.9744585
X-RAY DIFFRACTIONr_angle_other_deg0.9237441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9635452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.98621.407135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08815482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.791542
X-RAY DIFFRACTIONr_chiral_restr0.0640.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213894
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02756
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_it1.8362.7621817
X-RAY DIFFRACTIONr_mcbond_other1.8362.761816
X-RAY DIFFRACTIONr_mcangle_it2.3044.1322266
X-RAY DIFFRACTIONr_mcangle_other2.3044.1332267
X-RAY DIFFRACTIONr_scbond_it2.3633.1681547
X-RAY DIFFRACTIONr_scbond_other2.3583.1661542
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6614.6012316
X-RAY DIFFRACTIONr_long_range_B_refined3.95123.3873917
X-RAY DIFFRACTIONr_long_range_B_other3.41722.7133755
X-RAY DIFFRACTIONr_rigid_bond_restr1.53236625
X-RAY DIFFRACTIONr_sphericity_free26.0725104
X-RAY DIFFRACTIONr_sphericity_bonded8.2256797
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.191 105 -
Rwork0.142 2050 -
obs--99.91 %
Refinement TLS params.Method: refined / Origin x: 29.8128 Å / Origin y: 91.5301 Å / Origin z: 41.125 Å
111213212223313233
T0.0017 Å2-0.0003 Å2-0.0011 Å2-0.0055 Å2-0.0016 Å2--0.0023 Å2
L0.0571 °2-0.0431 °2-0.0079 °2-0.0484 °20.0064 °2--0.0012 °2
S-0.0049 Å °0.0018 Å °-0.0026 Å °0.0002 Å °0.0045 Å °0.003 Å °0.0005 Å °-0.0004 Å °0.0004 Å °

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