[English] 日本語
Yorodumi
- PDB-5on0: Crystal structure of NikA in complex with Fe-L2 (N-(2-hydroxy-3me... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5on0
TitleCrystal structure of NikA in complex with Fe-L2 (N-(2-hydroxy-3methoxybenzyl)-N-N'-ethylenediaminediacetic acid)
ComponentsNickel-binding periplasmic protein
KeywordsMETAL BINDING PROTEIN / artificial oxygenase / CLEC / dioxygen activation / oxidation of carbon-carbon double bonds
Function / homology
Function and homology information


nickel cation import across plasma membrane / metal cluster binding / nickel cation transport / peptide transport / peptide transmembrane transporter activity / negative chemotaxis / nickel cation binding / transition metal ion binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space ...nickel cation import across plasma membrane / metal cluster binding / nickel cation transport / peptide transport / peptide transmembrane transporter activity / negative chemotaxis / nickel cation binding / transition metal ion binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / periplasmic space / heme binding / membrane
Similarity search - Function
Nickel ABC transporter, substrate-binding protein NikA / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II ...Nickel ABC transporter, substrate-binding protein NikA / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9YH / ACETATE ION / : / Nickel-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCavazza, C. / Menage, S.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-14-CE06-0005-01 France
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Cross-Linked Artificial Enzyme Crystals as Heterogeneous Catalysts for Oxidation Reactions.
Authors: Lopez, S. / Rondot, L. / Lepretre, C. / Marchi-Delapierre, C. / Menage, S. / Cavazza, C.
History
DepositionAug 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Aug 19, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.5Jan 17, 2024Group: 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: Nickel-binding periplasmic protein
B: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,69733
Polymers112,7212
Non-polymers2,97531
Water16,051891
1
A: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,19221
Polymers56,3611
Non-polymers1,83120
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,50512
Polymers56,3611
Non-polymers1,14411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.937, 94.832, 124.993
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Nickel-binding periplasmic protein


Mass: 56360.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: nikA, b3476, JW3441 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33590

-
Non-polymers , 7 types, 922 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-9YH / 2-[2-[2-hydroxy-2-oxoethyl-[(3-methoxy-2-oxidanyl-phenyl)methyl]amino]ethyl-[(2-methylsulfanylphenyl)methyl]amino]ethanoic acid


Mass: 448.533 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H28N2O6S
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 891 / 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: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: sodium acetate, 100 mM, pH 4.6 Ammonium sulfate 1.8 M

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→47.416 Å / Num. obs: 81960 / % possible obs: 99.9 % / Redundancy: 7.35 % / Net I/σ(I): 14.58

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MVW

3mvw


Resolution: 1.9→47.416 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.87
RfactorNum. reflection% reflection
Rfree0.2066 4098 5 %
Rwork0.1763 --
obs0.1779 81931 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→47.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7808 0 187 891 8886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058226
X-RAY DIFFRACTIONf_angle_d0.89811204
X-RAY DIFFRACTIONf_dihedral_angle_d12.8253040
X-RAY DIFFRACTIONf_chiral_restr0.0361220
X-RAY DIFFRACTIONf_plane_restr0.0051462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92240.24241400.23042652X-RAY DIFFRACTION100
1.9224-1.94580.26121400.21872661X-RAY DIFFRACTION100
1.9458-1.97040.24461400.22182652X-RAY DIFFRACTION100
1.9704-1.99640.24741380.23132625X-RAY DIFFRACTION100
1.9964-2.02370.25521410.22052678X-RAY DIFFRACTION100
2.0237-2.05260.27281390.20712635X-RAY DIFFRACTION100
2.0526-2.08330.25591410.212686X-RAY DIFFRACTION100
2.0833-2.11580.25151400.20522650X-RAY DIFFRACTION100
2.1158-2.15050.23921400.19952664X-RAY DIFFRACTION100
2.1505-2.18760.22371400.19632666X-RAY DIFFRACTION100
2.1876-2.22740.25911390.2012631X-RAY DIFFRACTION100
2.2274-2.27020.24781420.19332699X-RAY DIFFRACTION100
2.2702-2.31660.24671380.19172631X-RAY DIFFRACTION100
2.3166-2.36690.21841400.18982663X-RAY DIFFRACTION100
2.3669-2.4220.23331410.18232673X-RAY DIFFRACTION100
2.422-2.48260.22271410.18532671X-RAY DIFFRACTION100
2.4826-2.54970.18961400.18672663X-RAY DIFFRACTION100
2.5497-2.62470.23921410.18142686X-RAY DIFFRACTION100
2.6247-2.70940.21551420.18932693X-RAY DIFFRACTION100
2.7094-2.80620.23311410.18322673X-RAY DIFFRACTION100
2.8062-2.91860.19691410.18412681X-RAY DIFFRACTION100
2.9186-3.05140.20261410.17612691X-RAY DIFFRACTION100
3.0514-3.21220.22521430.17482705X-RAY DIFFRACTION100
3.2122-3.41340.19521410.16542689X-RAY DIFFRACTION100
3.4134-3.67690.17461430.1592718X-RAY DIFFRACTION100
3.6769-4.04670.17391430.14092716X-RAY DIFFRACTION100
4.0467-4.63190.15491450.13862743X-RAY DIFFRACTION100
4.6319-5.8340.18421460.16322780X-RAY DIFFRACTION100
5.834-47.43070.19521510.18122858X-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