[English] 日本語
Yorodumi
- PDB-3zmi: Structure of E.coli rhomboid protease GlpG in complex with monoba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zmi
TitleStructure of E.coli rhomboid protease GlpG in complex with monobactam L29
ComponentsRHOMBOID PROTEASE GLPG
KeywordsHYDROLASE / INTRA-MEMBRANE PROTEASE / ACYL ENZYME / BETA LACTAMS / ANTIBIOTIC
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
Chem-L6C / Rhomboid protease GlpG
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVinothkumar, K.R. / Pierrat, O.A. / Large, J.M. / Freeman, M.
CitationJournal: Structure / Year: 2013
Title: Structure of Rhomboid Protease in Complex with Beta-Lactam Inhibitors Defines the S2' Cavity.
Authors: Vinothkumar, K.R. / Pierrat, O.A. / Large, J.M. / Freeman, M.
History
DepositionFeb 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Feb 27, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _citation.page_last / _exptl_crystal_grow.method ..._citation.page_last / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 20, 2023Group: 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 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RHOMBOID PROTEASE GLPG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3228
Polymers20,2141
Non-polymers2,1087
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)110.580, 110.580, 128.530
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: CORE TM DOMAIN, RESIDUES 92-270
Source method: isolated from a genetically manipulated source
Details: THE BETA LACTAM RING IS OPENED BY THE NUCLEOPHILIC ATTACK OF S201 ON C2-O1 TO FORM A COVALENT BOND
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P09391, rhomboid protease
#2: Chemical ChemComp-L6C / phenyl N-[(1R)-3-oxidanylidene-1-phenyl-propyl]carbamate


Mass: 269.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15NO3
#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.: 6
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details(3R)-3-(PHENOXYCARBONYLAMINO)-3-PHENYL- PROPANOIC ACID(L29): THE C2 CARBON IS COVALENTLY LINKED TO SER 201

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.8 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2M NACL, 0.1M BIS-TRIS, PH7.0, 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9786
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.2→55.29 Å / Num. obs: 15423 / % possible obs: 99.3 % / Redundancy: 5.2 % / Biso Wilson estimate: 43.23 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.8 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XOV

2xov


Resolution: 2.2→44.87 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 23.97 / Stereochemistry target values: ML
Details: RESIDUES 245-249 ARE DISORDERED. BNG 407 IS IN A SPECIAL POSITION AND REFINED WITH 0.5 OCCUPANCY.
RfactorNum. reflection% reflection
Rfree0.2609 778 5 %
Rwork0.2165 --
obs0.2186 15423 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1383 0 59 30 1472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081498
X-RAY DIFFRACTIONf_angle_d1.0532024
X-RAY DIFFRACTIONf_dihedral_angle_d12.727507
X-RAY DIFFRACTIONf_chiral_restr0.072216
X-RAY DIFFRACTIONf_plane_restr0.005237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.33780.29771390.24132421X-RAY DIFFRACTION100
2.3378-2.51830.25441380.2242416X-RAY DIFFRACTION100
2.5183-2.77170.27051270.21062439X-RAY DIFFRACTION100
2.7717-3.17270.26191350.2062444X-RAY DIFFRACTION100
3.1727-3.99690.2581160.20562483X-RAY DIFFRACTION100
3.9969-44.87930.25491230.22382442X-RAY DIFFRACTION95

+
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