[English] 日本語
Yorodumi
- PDB-5mt8: Structure of E.coli GlpG in complex with peptide derived inhibito... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mt8
TitleStructure of E.coli GlpG in complex with peptide derived inhibitor Ac-RVRHA-cmk
Components
  • ACE-ARG-VAL-ARG-HIS-ALA-0QE
  • Rhomboid protease GlpG
KeywordsHYDROLASE / Membrane protein / Intramembrane protease
Function / homology
Function and homology information


rhomboid protease / endopeptidase activity / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane
Similarity search - Function
Rhomboid-like fold / Rhomboid-like / Peptidase S54, GlpG peptidase, N-terminal / Rhomboid protease GlpG / GlpG peptidase, N-terminal domain superfamily / Cytoplasmic N-terminal domain of rhomboid serine protease / Peptidase S54, rhomboid domain / Rhomboid domain / Rhomboid-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Rhomboid protease GlpG
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Providencia stuartii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsVinothkumar, K.R.
CitationJournal: Cell Chem Biol / Year: 2017
Title: General and Modular Strategy for Designing Potent, Selective, and Pharmacologically Compliant Inhibitors of Rhomboid Proteases.
Authors: Ticha, A. / Stanchev, S. / Vinothkumar, K.R. / Mikles, D.C. / Pachl, P. / Began, J. / Skerle, J. / Svehlova, K. / Nguyen, M.T.N. / Verhelst, S.H.L. / Johnson, D.C. / Bachovchin, D.A. / ...Authors: Ticha, A. / Stanchev, S. / Vinothkumar, K.R. / Mikles, D.C. / Pachl, P. / Began, J. / Skerle, J. / Svehlova, K. / Nguyen, M.T.N. / Verhelst, S.H.L. / Johnson, D.C. / Bachovchin, D.A. / Lepsik, M. / Majer, P. / Strisovsky, K.
History
DepositionJan 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_validate_close_contact / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rhomboid protease GlpG
B: ACE-ARG-VAL-ARG-HIS-ALA-0QE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4818
Polymers20,9132
Non-polymers1,5676
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-1 kcal/mol
Surface area9830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.159, 111.159, 124.553
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein Rhomboid protease GlpG / Intramembrane serine protease


Mass: 20214.020 Da / Num. of mol.: 1 / Fragment: UNP Residues 92-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: glpG, b3424, JW5687 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P09391, rhomboid protease
#2: Protein/peptide ACE-ARG-VAL-ARG-HIS-ALA-0QE


Mass: 699.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Providencia stuartii (bacteria)
#3: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2M Sodium cholride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.95→44.9 Å / Num. obs: 21621 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.031 / Net I/σ(I): 24.5
Reflection shellResolution: 1.95→2 Å / Redundancy: 6 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.593 / % possible all: 95.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XOV

2xov


Resolution: 1.95→44.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / SU B: 7.073 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.122 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22507 1049 4.9 %RANDOM
Rwork0.19958 ---
obs0.20075 20568 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0.25 Å20 Å2
2---0.49 Å20 Å2
3---1.6 Å2
Refinement stepCycle: 1 / Resolution: 1.95→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 0 35 29 1531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191547
X-RAY DIFFRACTIONr_bond_other_d0.0010.021499
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.9392088
X-RAY DIFFRACTIONr_angle_other_deg0.89733419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2135182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.03721.55258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.1815233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.922157
X-RAY DIFFRACTIONr_chiral_restr0.0790.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021665
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02370
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_it3.3914.257736
X-RAY DIFFRACTIONr_mcbond_other3.3764.256735
X-RAY DIFFRACTIONr_mcangle_it4.1976.351916
X-RAY DIFFRACTIONr_mcangle_other4.26.351917
X-RAY DIFFRACTIONr_scbond_it4.785.004811
X-RAY DIFFRACTIONr_scbond_other4.7775.009812
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0647.2521175
X-RAY DIFFRACTIONr_long_range_B_refined8.88751.0011837
X-RAY DIFFRACTIONr_long_range_B_other8.88951.0111836
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.952→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 77 -
Rwork0.302 1431 -
obs--96.17 %
Refinement TLS params.Method: refined / Origin x: -17.7169 Å / Origin y: 7.658 Å / Origin z: -43.6524 Å
111213212223313233
T0.0258 Å20.018 Å20.0063 Å2-0.1092 Å2-0.0641 Å2--0.0568 Å2
L1.2561 °2-0.3219 °20.224 °2-0.2117 °2-0.351 °2--0.8599 °2
S0.0159 Å °0.0531 Å °-0.0046 Å °0.0365 Å °0.0114 Å °-0.0067 Å °-0.0594 Å °0.0661 Å °-0.0273 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A92 - 270
2X-RAY DIFFRACTION1B1 - 7

+
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