[English] 日本語
Yorodumi
- PDB-4oet: Crystal structure of NikZ from Campylobacter jejuni, unliganded form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4oet
TitleCrystal structure of NikZ from Campylobacter jejuni, unliganded form
ComponentsPutative peptide ABC-transport system periplasmic peptide-binding protein
KeywordsTRANSPORT PROTEIN / Extracytoplasmic / Nickel import / Metal transport / ABC-type importer / extracytoplasmic nickel-binding protein
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space / metal ion binding
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / 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 ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / 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 / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptide ABC-transport system periplasmic peptide-binding protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement-SAD / Resolution: 2.4 Å
AuthorsLebrette, H. / Cavazza, C.
CitationJournal: Structure / Year: 2014
Title: Promiscuous nickel import in human pathogens: structure, thermodynamics, and evolution of extracytoplasmic nickel-binding proteins.
Authors: Lebrette, H. / Brochier-Armanet, C. / Zambelli, B. / de Reuse, H. / Borezee-Durant, E. / Ciurli, S. / Cavazza, C.
History
DepositionJan 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Apr 18, 2018Group: Advisory / Data collection / Category: diffrn_detector / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_detector.detector
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Putative peptide ABC-transport system periplasmic peptide-binding protein
B: Putative peptide ABC-transport system periplasmic peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,36810
Polymers113,6312
Non-polymers7378
Water7,782432
1
A: Putative peptide ABC-transport system periplasmic peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3687
Polymers56,8151
Non-polymers5536
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative peptide ABC-transport system periplasmic peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0003
Polymers56,8151
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.060, 85.210, 148.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Putative peptide ABC-transport system periplasmic peptide-binding protein / NikZ


Mass: 56815.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: subsp. jejuni NCTC 11168 = ATCC 700819 / Gene: Cj1584c / Production host: Escherichia coli (E. coli) / References: UniProt: Q0P844
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15 % PEG 5000, 100 mM HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.00446 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00446 Å / Relative weight: 1
ReflectionResolution: 2.4→46.06 Å / Num. all: 40944 / Num. obs: 40880 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rsym value: 0.113 / Net I/σ(I): 14.29
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 4.15 / Rsym value: 0.505 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: molecular replacement-SAD
Starting model: PDB ENTRY 1DPE

1dpe


Resolution: 2.4→46.058 Å / SU ML: 0.23 / σ(F): 1.36 / Phase error: 20.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 2044 5 %
Rwork0.1793 --
obs0.1814 40880 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→46.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8050 0 48 432 8530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058300
X-RAY DIFFRACTIONf_angle_d0.90211208
X-RAY DIFFRACTIONf_dihedral_angle_d14.4013056
X-RAY DIFFRACTIONf_chiral_restr0.0391188
X-RAY DIFFRACTIONf_plane_restr0.0051434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.45580.28691330.23742530X-RAY DIFFRACTION99
2.4558-2.51720.2721330.22522532X-RAY DIFFRACTION100
2.5172-2.58530.24761350.21582556X-RAY DIFFRACTION100
2.5853-2.66140.28821340.21222559X-RAY DIFFRACTION100
2.6614-2.74720.24361350.2112554X-RAY DIFFRACTION100
2.7472-2.84540.25281330.21042544X-RAY DIFFRACTION100
2.8454-2.95930.26211370.20232592X-RAY DIFFRACTION100
2.9593-3.0940.26081360.20612586X-RAY DIFFRACTION100
3.094-3.25710.24891350.1932560X-RAY DIFFRACTION100
3.2571-3.46110.18931360.1722580X-RAY DIFFRACTION100
3.4611-3.72820.2061360.162596X-RAY DIFFRACTION100
3.7282-4.10320.18761370.14892592X-RAY DIFFRACTION100
4.1032-4.69640.18041380.13942633X-RAY DIFFRACTION100
4.6964-5.9150.19561400.16682656X-RAY DIFFRACTION100
5.915-46.06640.19531460.16812766X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6329-3.08750.67074.87970.95491.15460.1022-0.20550.3897-0.3989-0.2403-0.6935-0.01190.10450.12290.25350.00910.03430.2756-0.00990.197735.814264.860620.9181
21.7986-0.10630.44831.3829-0.79911.9144-0.0454-0.28110.27990.05950.02020.1004-0.178-0.24920.04340.17530.0155-0.00740.249-0.07530.307225.633974.826710.1003
31.28960.39490.23070.9721-0.20440.889-0.0084-0.0284-0.0108-0.0156-0.0266-0.1085-0.08220.01260.04320.18210.02140.00330.1283-0.0320.136454.151774.686510.347
41.65841.04462.05993.22532.03212.76840.00610.1469-0.22460.0699-0.0145-0.1502-0.11570.21010.07440.2923-0.05020.07830.31060.01050.232279.858469.832533.1453
51.2180.474-0.20440.92560.5362.64140.03590.23360.0484-0.09690.2582-0.2433-0.36510.5215-0.26090.2024-0.06020.04270.3173-0.06380.342487.171171.304549.2588
61.0410.26831.01371.19850.19672.58550.0668-0.1509-0.0609-0.01970.03390.10490.1032-0.4163-0.07390.1824-0.03080.00470.1750.03130.203360.230664.241644.1971
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 178 )
3X-RAY DIFFRACTION3chain 'A' and (resid 179 through 494 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 27 )
5X-RAY DIFFRACTION5chain 'B' and (resid 28 through 178 )
6X-RAY DIFFRACTION6chain 'B' and (resid 179 through 494 )

+
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