[English] 日本語
Yorodumi
- PDB-1t7d: Crystal structure of Escherichia coli type I signal peptidase in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1t7d
TitleCrystal structure of Escherichia coli type I signal peptidase in complex with a lipopeptide inhibitor
Components
  • ARYLOMYCIN A2
  • SIGNAL PEPTIDASE I
KeywordsHYDROLASE/ANTIBIOTIC / SIGNAL PEPTIDASE / SER/LYS DYAD / HYDROLASE / LIPOPEPTIDE / ANTIBIOTIC / BIARYL BRIDGE / HYDROLASE-ANTIBIOTIC COMPLEX
Function / homology
Function and homology information


signal peptidase I / signal peptide processing / protein processing / peptidase activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / plasma membrane
Similarity search - Function
Signal Peptidase I; Chain: A, domain 2 / Signal Peptidase I; Chain: A, domain 2 - #10 / Signal peptidase I, all-beta subdomain / Peptidase S26A, signal peptidase I, lysine active site / Signal peptidases I lysine active site. / Peptidase S26A, signal peptidase I / Signal peptidase, peptidase S26 / Peptidase S26A, signal peptidase I, conserved site / Signal peptidases I signature 3. / Peptidase S26A, signal peptidase I, serine active site ...Signal Peptidase I; Chain: A, domain 2 / Signal Peptidase I; Chain: A, domain 2 - #10 / Signal peptidase I, all-beta subdomain / Peptidase S26A, signal peptidase I, lysine active site / Signal peptidases I lysine active site. / Peptidase S26A, signal peptidase I / Signal peptidase, peptidase S26 / Peptidase S26A, signal peptidase I, conserved site / Signal peptidases I signature 3. / Peptidase S26A, signal peptidase I, serine active site / Signal peptidases I serine active site. / Peptidase S26 / Umud Fragment, subunit A / Umud Fragment, subunit A / LexA/Signal peptidase-like superfamily / Beta Complex / Ribbon / Mainly Beta
Similarity search - Domain/homology
ARYLOMYCIN A2 / 10-METHYLUNDECANOIC ACID / : / Signal peptidase I
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
STREPTOMYCES TU (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsPaetzel, M. / Goodall, J.J. / Kania, M. / Dalbey, R.E. / Page, M.G.P.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Crystallographic and Biophysical Analysis of a Bacterial Signal Peptidase in Complex with a Lipopeptide Based Inhibitor.
Authors: Paetzel, M. / Goodall, J.J. / Kania, M. / Dalbey, R.E. / Page, M.G.P.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: Crystal Structure of a Bacterial Signal Peptidase Apoenzyme: Implications for Signal Peptide Binding and the Ser-Lys Dyad Mechanism
Authors: Paetzel, M. / Dalbey, R.E. / Strynadka, N.C.
#2: Journal: Nature / Year: 1998
Title: Crystal Structure of a Bacterial Signal Peptidase in Complex with a Beta-Lactam Inhibitor.
Authors: Paetzel, M. / Dalbey, R.E. / Strynadka, N.C.
History
DepositionMay 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 2.0Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / 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 / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SIGNAL PEPTIDASE I
B: SIGNAL PEPTIDASE I
C: ARYLOMYCIN A2
D: ARYLOMYCIN A2
C: 10-METHYLUNDECANOIC ACID
D: 10-METHYLUNDECANOIC ACID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8506
Polymers57,4494
Non-polymers4012
Water4,774265
1
B: SIGNAL PEPTIDASE I
D: ARYLOMYCIN A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9253
Polymers28,7242
Non-polymers2001
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-4.5 kcal/mol
Surface area11140 Å2
MethodPISA
2
A: SIGNAL PEPTIDASE I
C: ARYLOMYCIN A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9253
Polymers28,7242
Non-polymers2001
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-4.6 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.609, 69.609, 258.466
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a monomer

-
Components

#1: Protein SIGNAL PEPTIDASE I / / SPASE I / LEADER PEPTIDASE I


Mass: 28079.814 Da / Num. of mol.: 2 / Fragment: RESIDUES 76-324
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Gene: LEPB / Plasmid: PET3D / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00803, signal peptidase I
#2: Protein/peptide ARYLOMYCIN A2 / /


Type: Lipopeptide / Class: Antibiotic / Mass: 644.674 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: ARYLOMYCIN A2 IS A BIARYL-BRIDGED LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) N-TERM EXOCYCLIC TRIPEPTIDE (2) A TRICYCLIC PEPTIDE, WITH [3,3] BIARYL BOND BETWEEN RESIDUE 4 AND 6 AN ...Details: ARYLOMYCIN A2 IS A BIARYL-BRIDGED LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) N-TERM EXOCYCLIC TRIPEPTIDE (2) A TRICYCLIC PEPTIDE, WITH [3,3] BIARYL BOND BETWEEN RESIDUE 4 AND 6 AN ISO-C12 FATTY ACID IS LINKED TO RESIDUE 1.
Source: (natural) STREPTOMYCES TU (bacteria) / References: NOR: NOR01115, ARYLOMYCIN A2
#3: Chemical
ChemComp-M12 / 10-METHYLUNDECANOIC ACID /


Type: Lipopeptide / Class: Antibiotic / Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2
Details: ARYLOMYCIN A2 IS A BIARYL-BRIDGED LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) N-TERM EXOCYCLIC TRIPEPTIDE (2) A TRICYCLIC PEPTIDE, WITH [3,3] BIARYL BOND BETWEEN RESIDUE 4 AND 6 AN ...Details: ARYLOMYCIN A2 IS A BIARYL-BRIDGED LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) N-TERM EXOCYCLIC TRIPEPTIDE (2) A TRICYCLIC PEPTIDE, WITH [3,3] BIARYL BOND BETWEEN RESIDUE 4 AND 6 AN ISO-C12 FATTY ACID IS LINKED TO RESIDUE 1.
References: ARYLOMYCIN A2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Compound detailsARYLOMYCIN A2 IS A CYCLIC LIPOHEXAPEPTIDE, A MEMBER OF THE ARYLOMYCIN FAMILY. ALL MEMBERS HAVE A ...ARYLOMYCIN A2 IS A CYCLIC LIPOHEXAPEPTIDE, A MEMBER OF THE ARYLOMYCIN FAMILY. ALL MEMBERS HAVE A FATTY ACID AT THE N-TERM AND A CORE STRUCTURE OF TRIPEPTIDE MACROCYCLE FORMED BY A C-C BIARYL LINKAGE BETWEEN RESIDUES 4 AND 6. HERE, ARYLOMYCIN A2 IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND ONE LIGAND (HET) M12.
Sequence detailsTHE PROTEIN IS A SOLUBLE CATALYTICALLY ACTIVE FRAGMENT OF THE ESCHERICHIA COLI TYPE I SIGNAL ...THE PROTEIN IS A SOLUBLE CATALYTICALLY ACTIVE FRAGMENT OF THE ESCHERICHIA COLI TYPE I SIGNAL PEPTIDASE (DELTA 2-75). IT LACKS THE RESIDUES CORRESPONDING TO THE TWO TRANSMEMBRANE SEGMENTS (RESIDUES 4-28 AND 58-76) AND A SMALL CYTOPLASMIC REGION (RESIDUES 29-58).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 6
Details: 0.5% TRITON X-100, 15% PEG 4000, 20% PROPANOL, 0.1 M SODIUM CITRATE, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.47→40 Å / Num. obs: 21589 / % possible obs: 90.9 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 19.4
Reflection shellResolution: 2.47→2.56 Å / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 8 / % possible all: 86.4

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B12

1b12


Resolution: 2.47→29.54 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2098721.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2142 9.9 %RANDOM
Rwork0.23 ---
obs0.23 21584 90.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.11 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 49.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.48 Å20 Å20 Å2
2--6.48 Å20 Å2
3----12.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.47→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 6 265 3766
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.711.5
X-RAY DIFFRACTIONc_mcangle_it3.042
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 2.47→2.62 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 334 10.2 %
Rwork0.311 2952 -
obs--85.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4DRGCNS.PARDRGCNS.TOP

+
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