[English] 日本語
Yorodumi
- PDB-1i78: CRYSTAL STRUCTURE OF OUTER MEMBRANE PROTEASE OMPT FROM ESCHERICHI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i78
TitleCRYSTAL STRUCTURE OF OUTER MEMBRANE PROTEASE OMPT FROM ESCHERICHIA COLI
ComponentsPROTEASE VII
KeywordsHYDROLASE / integral outer membrane protein / protease / beta barrel
Function / homology
Function and homology information


omptin / cell outer membrane / endopeptidase activity / aspartic-type endopeptidase activity / serine-type endopeptidase activity / proteolysis
Similarity search - Function
OMPT-like / Aspartyl proteases, omptin family signature 2. / Peptidase A26, omptin / Peptidase A26, omptin, conserved site / : / Omptin family / Aspartyl proteases, omptin family signature 1. / Outer membrane adhesin/peptidase omptin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsVandeputte-Rutten, L. / Kramer, R.A. / Kroon, J. / Dekker, N. / Egmond, M.R. / Gros, P.
CitationJournal: EMBO J. / Year: 2001
Title: Crystal structure of the outer membrane protease OmpT from Escherichia coli suggests a novel catalytic site.
Authors: Vandeputte-Rutten, L. / Kramer, R.A. / Kroon, J. / Dekker, N. / Egmond, M.R. / Gros, P.
History
DepositionMar 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jul 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 1.4Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEASE VII
B: PROTEASE VII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3978
Polymers66,9912
Non-polymers1,4066
Water52229
1
A: PROTEASE VII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3175
Polymers33,4961
Non-polymers8214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PROTEASE VII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0803
Polymers33,4961
Non-polymers5852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-37 kcal/mol
Surface area28490 Å2
MethodPISA
4
B: PROTEASE VII
hetero molecules

A: PROTEASE VII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3978
Polymers66,9912
Non-polymers1,4066
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_665x-y+1,-y+1,-z+1/31
Buried area3260 Å2
ΔGint-27 kcal/mol
Surface area28180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.389, 98.389, 165.695
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsOmpT is active as a monomer. The assymetric unit contains two monomers.

-
Components

#1: Protein PROTEASE VII / OMPT / OMPTIN / OUTER MEMBRANE PROTEIN 3B


Mass: 33495.594 Da / Num. of mol.: 2 / Mutation: S99A,G216K,K217G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: OMPT / Plasmid: PRAK11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09169, EC: 3.4.21.87
#2: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 3.45 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 30% (v/v) 2-methyl-2,4-pentanediol, 0.3 M sodium citrate PH 5.5, 1% (w/v) octyl-beta-D-glucopyranoside, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 %(w/v)octyl-beta-D-glucopyranoside11
230 %(v/v)MPD11
30.3 Msodium citrate11

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9322 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 9, 1999 / Details: toroidal mirror
RadiationMonochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9322 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 29075 / Num. obs: 27400 / % possible obs: 94.3 % / Redundancy: 1.59 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 8.82
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 1.57 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 2.54 / Num. unique all: 2766 / % possible all: 96.1
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 43471
Reflection shell
*PLUS
Lowest resolution: 2.69 Å / % possible obs: 97.7 % / Num. unique obs: 2766 / Num. measured obs: 4352

-
Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1407 -RANDOM
Rwork0.238 ---
all-27389 --
obs-27389 94.2 %-
Displacement parametersBiso mean: 53 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.02 Å20.04 Å2
2--0.74 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4609 0 96 29 4734
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.022
RfactorNum. reflection% reflection
Rfree0.36 270 -
Rwork0.318 --
obs-4314 96.1 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Rfactor obs: 0.238 / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 53 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shell
*PLUS
Highest resolution: 2.6 Å / Rfactor Rfree: 0.36 / Rfactor Rwork: 0.318

+
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