[English] 日本語
Yorodumi
- PDB-6aem: Crystal structure of the PKD1 domain of Vibrio anguillarum Epp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6aem
TitleCrystal structure of the PKD1 domain of Vibrio anguillarum Epp
ComponentsPKD domain
KeywordsUNKNOWN FUNCTION / protease / polycystic kidney disease domain
Function / homology
Function and homology information


Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesVibrio anguillarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.272 Å
AuthorsMa, Q. / Li, P.
Funding support China, 2items
OrganizationGrant numberCountry
1000 talent program China
Chinese Academy of Sciences100 talent program China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structural basis for specific calcium binding by the polycystic-kidney-disease domain of Vibrio anguillarum protease Epp
Authors: Li, P. / Zang, K. / Li, Y. / Liu, C. / Ma, Q.
History
DepositionAug 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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 / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PKD domain
B: PKD domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2859
Polymers18,8782
Non-polymers4077
Water3,405189
1
A: PKD domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6755
Polymers9,4391
Non-polymers2364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PKD domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6104
Polymers9,4391
Non-polymers1713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.096, 46.069, 41.616
Angle α, β, γ (deg.)90.00, 97.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-103-

ZN

21A-232-

HOH

31A-233-

HOH

41B-236-

HOH

-
Components

#1: Protein PKD domain


Mass: 9439.089 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio anguillarum (bacteria) / Plasmid: pETM11 vector (EMBL) / Cell line (production host): Rosetta(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A383R4X5*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE GENEBANK accession number is AQM04426.1 (sequence 756-838) for this sequence.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 21mg/ml protein in 10 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM DTT was mixed with 0.1 M sodium cacodylate pH 6.5, 18% PEG8000 (w/v), 0.2 M zinc acetate in 1:1 volume ratio

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.272→38.566 Å / Num. obs: 33927 / % possible obs: 96.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 13.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.027 / Rrim(I) all: 0.07 / Net I/σ(I): 19.3
Reflection shellResolution: 1.272→1.277 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.924 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 308 / CC1/2: 0.771 / Rpim(I) all: 0.381 / Rrim(I) all: 1.001 / % possible all: 85.3

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSNov 11, 2017, built on 20171111data reduction
Aimless(version 0.5.29), CCP4 7.0.026data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L9D

4l9d


Resolution: 1.272→35.253 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.06
RfactorNum. reflection% reflectionSelection details
Rfree0.1862 1705 5.03 %random
Rwork0.1508 ---
obs0.1526 33921 96.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18 Å2
Refinement stepCycle: LAST / Resolution: 1.272→35.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 7 189 1488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011352
X-RAY DIFFRACTIONf_angle_d1.1471860
X-RAY DIFFRACTIONf_dihedral_angle_d16.914478
X-RAY DIFFRACTIONf_chiral_restr0.086209
X-RAY DIFFRACTIONf_plane_restr0.007248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2723-1.30970.30461270.26642554X-RAY DIFFRACTION93
1.3097-1.3520.27571440.24042619X-RAY DIFFRACTION95
1.352-1.40030.29351350.23712675X-RAY DIFFRACTION96
1.4003-1.45640.26741180.21582650X-RAY DIFFRACTION95
1.4564-1.52270.2251600.16962653X-RAY DIFFRACTION97
1.5227-1.6030.20891450.15162699X-RAY DIFFRACTION97
1.603-1.70340.18271390.14272668X-RAY DIFFRACTION96
1.7034-1.83490.19251330.1372723X-RAY DIFFRACTION98
1.8349-2.01960.18291510.13272737X-RAY DIFFRACTION99
2.0196-2.31170.16371300.12952726X-RAY DIFFRACTION98
2.3117-2.91230.1831550.14462748X-RAY DIFFRACTION99
2.9123-35.26620.15641680.14162764X-RAY DIFFRACTION97

+
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