[English] 日本語
Yorodumi
- PDB-4lp1: Crystal structure of CyaY protein from Psychromonas ingrahamii in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lp1
TitleCrystal structure of CyaY protein from Psychromonas ingrahamii in complex with Eu(III)
ComponentsProtein CyaY
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


iron-sulfur cluster assembly / ferric iron binding / ferrous iron binding / cytosol
Similarity search - Function
: / Frataxin/CyaY / Metal Transport, Frataxin; Chain A / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Frataxin/CyaY superfamily ...: / Frataxin/CyaY / Metal Transport, Frataxin; Chain A / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Frataxin/CyaY superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
EUROPIUM (III) ION / Iron-sulfur cluster assembly protein CyaY
Similarity search - Component
Biological speciesPsychromonas ingrahamii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsNoguera, M.E. / Roman, E.A. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Santos, J.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2015
Title: Structural characterization of metal binding to a cold-adapted frataxin
Authors: Noguera, M.E. / Roman, E.A. / Rigal, J.B. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Santos, J.
History
DepositionJul 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Nov 8, 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 / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein CyaY
B: Protein CyaY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,95811
Polymers24,5912
Non-polymers1,3689
Water81145
1
A: Protein CyaY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9035
Polymers12,2951
Non-polymers6084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein CyaY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0556
Polymers12,2951
Non-polymers7605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.821, 49.992, 46.580
Angle α, β, γ (deg.)90.000, 90.430, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Protein CyaY


Mass: 12295.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychromonas ingrahamii (bacteria) / Strain: 37 / Gene: cyaY, Ping_0042 / Plasmid: pJexpress411:56977 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A1SR01
#2: Chemical
ChemComp-EU3 / EUROPIUM (III) ION


Mass: 151.964 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Eu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 1.89 Å3/Da / Density % sol: 34.76 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 20mM sodium acetate, 200mM MgCl2, 29.5% PEG 4000, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.91907 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 2, 2012
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91907 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 30293 / Num. obs: 30293 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Rmerge(I) obs: 0.039 / Χ2: 1.052 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.861.60.29829351.012189.8
1.86-1.941.60.20930211.086191.4
1.94-2.031.60.13830501.078192.2
2.03-2.131.50.10329771.085190.1
2.13-2.271.60.07530821.026193.5
2.27-2.441.70.0631801.048195.4
2.44-2.691.70.05230941.01194.3
2.69-3.081.70.03931301.068194.4
3.08-3.881.60.02730631.037193
3.88-501.60.01927611.076183.3

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.8.2_1309refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HS5

4hs5


Resolution: 1.803→31.147 Å / Occupancy max: 1 / Occupancy min: 0.28 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.62 / Stereochemistry target values: ML
Details: NUMBER UNIQUE REFLECTIONS (ALL): ANOMALOUS PAIRS TREATED SEPARATELY. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2602 814 5.07 %RANDOM
Rwork0.2135 ---
obs0.2158 16054 94.37 %-
all-30293 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.85 Å2 / Biso mean: 33.4858 Å2 / Biso min: 8.63 Å2
Refinement stepCycle: LAST / Resolution: 1.803→31.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 9 45 1772
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.235
X-RAY DIFFRACTIONf_dihedral_angle_d13.306
X-RAY DIFFRACTIONf_chiral_restr0.052
X-RAY DIFFRACTIONf_plane_restr0.005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.8026-1.91550.31731090.2519X-RAY DIFFRACTION686
1.9155-2.06340.26411370.2255X-RAY DIFFRACTION695
2.0634-2.2710.27681450.2187X-RAY DIFFRACTION696
2.271-2.59940.24831360.2219X-RAY DIFFRACTION698
2.5994-3.27450.28691530.2326X-RAY DIFFRACTION699
3.2745-31.15150.23651340.1919X-RAY DIFFRACTION693

+
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