[English] 日本語
Yorodumi
- PDB-5inr: A C69-family cysteine dipeptidase in complex with Ala-Pro from La... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5inr
TitleA C69-family cysteine dipeptidase in complex with Ala-Pro from Lactobacillus farciminis
ComponentsDipeptidase
KeywordsHYDROLASE / C69 family / cysteine dipeptidase / Ntn hydrolase / Lactobacillus farciminis / Gly-Pro
Function / homologyACETATE ION / ALANINE / PROLINE / :
Function and homology information
Biological speciesLactobacillus farciminis KCTC 3681 = DSM 20184 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.652 Å
AuthorsKono, R. / Watanabe, K.
CitationJournal: To Be Published
Title: A C69-family cysteine dipeptidase from Lactobacillus farciminis; substrate recognition mechanism and autoproteolytic mechanism in enzyme maturation
Authors: Kono, R. / Watanabe, K.
History
DepositionMar 7, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dipeptidase
B: Dipeptidase
C: Dipeptidase
D: Dipeptidase
E: Dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,77451
Polymers264,5225
Non-polymers3,25346
Water50,9822830
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-54 kcal/mol
Surface area86380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.398, 182.299, 98.335
Angle α, β, γ (deg.)90.00, 112.84, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 5 molecules ABCDE

#1: Protein
Dipeptidase


Mass: 52904.344 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus farciminis KCTC 3681 = DSM 20184 (bacteria)
Strain: KCTC 3681 = DSM 20184 / Gene: FC68_GL001211 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0R1IQH8

-
Non-polymers , 5 types, 2876 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical
ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H9NO2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2830 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsALA 501-PRO 502 is Substrate analoge

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 0.8 M 1,6-hexanediol, 10 mM CoCl2, 100 mM acetate buffer

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Sep 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→39.3 Å / Num. obs: 321818 / % possible obs: 99.2 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 26.14
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 3.93 / % possible all: 65.9

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IAU

5iau


Resolution: 1.652→39.254 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.33
RfactorNum. reflection% reflection
Rfree0.1822 16098 5.01 %
Rwork0.1588 --
obs0.16 321437 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.652→39.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18370 0 144 2830 21344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00719002
X-RAY DIFFRACTIONf_angle_d1.07325839
X-RAY DIFFRACTIONf_dihedral_angle_d11.9016965
X-RAY DIFFRACTIONf_chiral_restr0.0452824
X-RAY DIFFRACTIONf_plane_restr0.0053444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6517-1.67050.21985130.20079704X-RAY DIFFRACTION95
1.6705-1.69010.23745600.19410062X-RAY DIFFRACTION99
1.6901-1.71080.23215160.19410095X-RAY DIFFRACTION99
1.7108-1.73240.21894870.182510204X-RAY DIFFRACTION99
1.7324-1.75520.20324960.175110229X-RAY DIFFRACTION99
1.7552-1.77930.20444980.175310100X-RAY DIFFRACTION99
1.7793-1.80470.20855490.171810120X-RAY DIFFRACTION99
1.8047-1.83160.19955590.170710162X-RAY DIFFRACTION99
1.8316-1.86020.19175340.172210165X-RAY DIFFRACTION99
1.8602-1.89070.19525580.167710096X-RAY DIFFRACTION99
1.8907-1.92330.18935470.165110203X-RAY DIFFRACTION99
1.9233-1.95830.18625740.159810101X-RAY DIFFRACTION99
1.9583-1.9960.19345520.162210210X-RAY DIFFRACTION100
1.996-2.03670.19165180.160710189X-RAY DIFFRACTION100
2.0367-2.0810.1815500.154110166X-RAY DIFFRACTION100
2.081-2.12940.17435440.153510214X-RAY DIFFRACTION100
2.1294-2.18260.18075210.152210237X-RAY DIFFRACTION100
2.1826-2.24160.2015280.162510189X-RAY DIFFRACTION100
2.2416-2.30760.18275350.154610242X-RAY DIFFRACTION100
2.3076-2.38210.18635570.155810199X-RAY DIFFRACTION100
2.3821-2.46720.19375210.159710276X-RAY DIFFRACTION100
2.4672-2.5660.18755670.158610180X-RAY DIFFRACTION100
2.566-2.68270.17785350.158810256X-RAY DIFFRACTION100
2.6827-2.82410.18515470.158810204X-RAY DIFFRACTION100
2.8241-3.0010.17955440.156310245X-RAY DIFFRACTION100
3.001-3.23260.17545480.156910240X-RAY DIFFRACTION100
3.2326-3.55770.17615270.153710274X-RAY DIFFRACTION100
3.5577-4.07210.16575360.143710251X-RAY DIFFRACTION100
4.0721-5.12860.14385290.13610273X-RAY DIFFRACTION100
5.1286-39.2650.16925480.17110253X-RAY DIFFRACTION99

+
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