[English] 日本語
Yorodumi
- PDB-7xrx: insulin-cleaving membrane protease-ICMP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xrx
Titleinsulin-cleaving membrane protease-ICMP
ComponentsInsulin-cleaving metalloproteinase outer membrane protein
KeywordsMETAL BINDING PROTEIN / Pseudomonas aeruginosa / metallopeptidase
Function / homologyImelysin-like domain / Imelysin-like domain superfamily / Imelysin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Insulin-cleaving metalloproteinase outer membrane protein
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.882 Å
AuthorsWang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystallization and X-ray diffraction analysis of native and selenomethionine-substituted ICMP from P. aeruginosa
Authors: Wang, J.
History
DepositionMay 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Insulin-cleaving metalloproteinase outer membrane protein
B: Insulin-cleaving metalloproteinase outer membrane protein
C: Insulin-cleaving metalloproteinase outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,1176
Polymers128,9973
Non-polymers1203
Water26,7881487
1
A: Insulin-cleaving metalloproteinase outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0392
Polymers42,9991
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area16220 Å2
MethodPISA
2
B: Insulin-cleaving metalloproteinase outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0392
Polymers42,9991
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area16080 Å2
MethodPISA
3
C: Insulin-cleaving metalloproteinase outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0392
Polymers42,9991
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area16080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.927, 78.141, 99.916
Angle α, β, γ (deg.)90.000, 113.520, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Insulin-cleaving metalloproteinase outer membrane protein


Mass: 42998.836 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: icmP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HW32
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1487 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 1.6 M sodium citrate tri-basic dihydrate at pH 6.5

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.882→34.372 Å / Num. obs: 97961 / % possible obs: 99.4 % / Redundancy: 5.8 % / CC1/2: 0.839 / Net I/σ(I): 14.3
Reflection shellResolution: 1.9→1.97 Å / Num. unique obs: 54651 / CC1/2: 0.839

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.882→34.372 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1865 4565 4.66 %
Rwork0.1459 93396 -
obs0.1479 97961 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.42 Å2 / Biso mean: 23.046 Å2 / Biso min: 2.26 Å2
Refinement stepCycle: final / Resolution: 1.882→34.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9015 0 3 1487 10505
Biso mean--20.88 34.03 -
Num. residues----1193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079171
X-RAY DIFFRACTIONf_angle_d0.83712415
X-RAY DIFFRACTIONf_chiral_restr0.0441364
X-RAY DIFFRACTIONf_plane_restr0.0041661
X-RAY DIFFRACTIONf_dihedral_angle_d14.5295495
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8821-1.90350.2202610.2014141544
1.9035-1.92590.26491370.1966309297
1.9259-1.94930.27751520.1897313898
1.9493-1.9740.24561430.1744308498
1.974-20.23181370.166316098
2-2.02740.22841520.1582312499
2.0274-2.05630.1921570.1566311598
2.0563-2.0870.20081520.1476313399
2.087-2.11960.19331560.1474317599
2.1196-2.15440.19011580.1394315399
2.1544-2.19150.21261470.145317599
2.1915-2.23140.18391460.1431315199
2.2314-2.27430.19111580.1432314999
2.2743-2.32070.1791430.1418320499
2.3207-2.37110.20321610.1455315999
2.3711-2.42630.19161680.1456313399
2.4263-2.4870.21071550.1461318399
2.487-2.55420.21851730.1467315699
2.5542-2.62930.18461440.1478318599
2.6293-2.71410.17361260.15383210100
2.7141-2.81110.19221400.1532319199
2.8111-2.92360.19141440.15053209100
2.9236-3.05660.191680.14963162100
3.0566-3.21760.19751600.153219100
3.2176-3.4190.18331780.13983192100
3.419-3.68270.15281880.13243174100
3.6827-4.05280.15381510.12713225100
4.0528-4.63810.15891450.12563248100
4.6381-5.83880.1811960.14883202100
5.8388-34.3720.17551690.15253280100

+
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://pdbjlc1.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