[English] 日本語
Yorodumi
- PDB-5lhj: Bottromycin maturation enzyme BotP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lhj
TitleBottromycin maturation enzyme BotP
ComponentsLeucine aminopeptidase 2, chloroplastic
KeywordsHYDROLASE / BotP / Bottromycin / RiPPs
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
Probable cytosol aminopeptidase
Similarity search - Component
Biological speciesStreptomyces sp. BC16019 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsKoehnke, J. / Mann, G.
Funding support Germany, United Kingdom, 2items
OrganizationGrant numberCountry
German Research FoundationKO4116/3-1 Germany
Wellcome Trust086036 United Kingdom
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 12, 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
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Leucine aminopeptidase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0624
Polymers51,6961
Non-polymers3663
Water8,719484
1
A: Leucine aminopeptidase 2, chloroplastic
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)312,37124
Polymers310,1766
Non-polymers2,19518
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/21
crystal symmetry operation11_454-x+y-1,y,-z-1/21
crystal symmetry operation12_554x,x-y,-z-1/21
Buried area24810 Å2
ΔGint-160 kcal/mol
Surface area91140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.420, 152.420, 100.896
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-1182-

HOH

-
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG 3350 (20 % (w/v)) and sodium malonate pH 7.0 (0.24 M)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.76→24.22 Å / Num. obs: 68447 / % possible obs: 99.96 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 17
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 3.3 / % possible all: 99.96

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→24.22 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.428 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.083 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1913 3440 5.1 %RANDOM
Rwork0.17635 ---
obs0.17713 64571 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.536 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0.2 Å20 Å2
2---0.4 Å20 Å2
3---1.29 Å2
Refinement stepCycle: 1 / Resolution: 1.76→24.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3250 0 17 484 3751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193325
X-RAY DIFFRACTIONr_bond_other_d0.0020.023243
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9784528
X-RAY DIFFRACTIONr_angle_other_deg0.92537402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6965448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.5621.385130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.87615476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3591541
X-RAY DIFFRACTIONr_chiral_restr0.0730.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02739
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_it0.8881.8431795
X-RAY DIFFRACTIONr_mcbond_other0.8861.8421794
X-RAY DIFFRACTIONr_mcangle_it1.5352.7512236
X-RAY DIFFRACTIONr_mcangle_other1.5352.7532237
X-RAY DIFFRACTIONr_scbond_it1.1712.0511530
X-RAY DIFFRACTIONr_scbond_other1.172.0511530
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.972.9962291
X-RAY DIFFRACTIONr_long_range_B_refined7.47317.7754061
X-RAY DIFFRACTIONr_long_range_B_other6.42115.7093726
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.805 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 263 -
Rwork0.233 4665 -
obs--99.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.22330.56190.10871.71910.68610.6457-0.00260.0168-0.033-0.07660.0338-0.0732-0.07170.0399-0.03120.02630.0288-0.0180.0737-0.03320.0341-27.7656-58.3138-22.2757
23.17290.7614-1.53650.6884-0.61821.0293-0.02050.0275-0.10510.08010.0288-0.05070.01180.0597-0.00830.02670.0237-0.02520.0603-0.02430.0513-34.7477-50.3049-11.8919
31.17970.20550.01660.19840.15010.1593-0.0646-0.1014-0.00360.06070.1163-0.01470.07660.113-0.05160.04330.0591-0.0260.12410.00080.0602-33.1021-53.644-6.7109
40.46990.03560.06730.27890.06780.1998-0.0916-0.0394-0.01340.08360.03070.01420.01680.01380.06090.06320.017-0.00120.05750.01280.0309-53.6173-38.2562.7003
50.1642-0.24350.25180.396-0.440.5156-0.05730.02650.04770.0278-0.0733-0.09710.01620.09610.13060.11130.03320.00740.0770.03090.0794-43.5769-37.938-2.4049
60.2985-0.2131-0.08950.2649-0.06240.190100.010.030.0155-0.0295-0.0407-0.03030.00270.02960.0425-0.0023-0.02860.0410.00510.0335-53.9633-29.9714-10.7723
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 125
2X-RAY DIFFRACTION2A126 - 142
3X-RAY DIFFRACTION3A143 - 175
4X-RAY DIFFRACTION4A176 - 273
5X-RAY DIFFRACTION5A274 - 307
6X-RAY DIFFRACTION6A308 - 499

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more