[English] 日本語
Yorodumi
- PDB-8gxv: Structure of a bacterial serpin Choloropin derived from Cholorobi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gxv
TitleStructure of a bacterial serpin Choloropin derived from Cholorobium limicola
ComponentsProteinase inhibitor I4 serpin
KeywordsDNA BINDING PROTEIN / Serpin / Serine Proteinase Inhibitor / Metastable conformation / DNA binding
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular space
Similarity search - Function
Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors
Similarity search - Domain/homology
Proteinase inhibitor I4 serpin
Similarity search - Component
Biological speciesChlorobium limicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhou, A. / Xu, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81870309 China
National Natural Science Foundation of China (NSFC)32070934 China
CitationJournal: To Be Published
Title: Climpin, a Novel Bacterial a Serpin inducing a Broad Range of Proteases and Regulated by Heparin and DNA.
Authors: Zhou, A. / Xu, J.
History
DepositionSep 21, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteinase inhibitor I4 serpin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0386
Polymers41,6851
Non-polymers3545
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-122 kcal/mol
Surface area15440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.660, 60.910, 130.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

-
Components

#1: Protein Proteinase inhibitor I4 serpin


Mass: 41684.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium limicola (strain DSM 245 / NBRC 103803 / 6330) (bacteria)
Gene: Clim_1363 / Production host: Escherichia coli (E. coli) / References: UniProt: B3ECZ8
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.35 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG MME 550, 0.1M MES pH 6.5, 0.01M Zinc Sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→60.91 Å / Num. obs: 25206 / % possible obs: 99.92 % / Redundancy: 2 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02969 / Net I/σ(I): 15.11
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 2453 / CC1/2: 0.959 / CC star: 0.989

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata scaling
Cootmodel building
REFMAC5.8.0256refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EE5

6ee5


Resolution: 2.2→60.91 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 1234 4.9 %
Rwork0.201 23960 -
obs0.2033 25194 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.57 Å2 / Biso mean: 30.4848 Å2 / Biso min: 14.97 Å2
Refinement stepCycle: final / Resolution: 2.2→60.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 10 59 2852
Biso mean--45.18 29.32 -
Num. residues----353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.290.28061220.208626052727
2.29-2.390.29121310.220126352766
2.39-2.520.32291300.221726382768
2.52-2.680.26491450.214425982743
2.68-2.880.28071640.220526292793
2.88-3.170.26761210.211726702791
3.17-3.630.22891500.194326492799
3.63-4.580.22141450.180926812826
4.58-60.910.21391260.194828552981
Refinement TLS params.Method: refined / Origin x: 2.7961 Å / Origin y: -20.5671 Å / Origin z: -21.0001 Å
111213212223313233
T0.1317 Å20.0164 Å20.0069 Å2-0.1729 Å2-0.0283 Å2--0.1362 Å2
L0.9714 °20.7537 °2-0.2834 °2-2.2018 °2-0.4933 °2--0.9484 °2
S0.1019 Å °-0.0391 Å °0.1051 Å °0.1097 Å °-0.0759 Å °0.1852 Å °-0.078 Å °-0.0112 Å °-0.0249 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 375
2X-RAY DIFFRACTION1allB2 - 64
3X-RAY DIFFRACTION1allC1 - 4
4X-RAY DIFFRACTION1allD1

+
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://pdbjlvh1.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