[English] 日本語
Yorodumi
- PDB-4oeu: Crystal structure of NikZ from Campylobacter jejuni in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4oeu
TitleCrystal structure of NikZ from Campylobacter jejuni in complex with Ni(L-His)
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


peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / 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
HISTIDINE / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Peptide ABC-transport system periplasmic peptide-binding protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.2Sep 20, 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_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.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.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: 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)114,76215
Polymers113,6312
Non-polymers1,13213
Water5,531307
1
A: Putative peptide ABC-transport system periplasmic peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3597
Polymers56,8151
Non-polymers5436
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative peptide ABC-transport system periplasmic peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4048
Polymers56,8151
Non-polymers5887
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.480, 72.770, 86.090
Angle α, β, γ (deg.)90.00, 111.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-503-

NI

-
Components

-
Protein , 1 types, 2 molecules AB

#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

-
Non-polymers , 6 types, 320 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N3O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 307 / 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: 1.97 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 % PEG 3350, 100 mM HEPES pH 7.0, 0.2 M MgCl2. Crystal soaking in a solution containing 1 mM NiCl2 and 2 mM L-His., VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97901 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 2.2→46.63 Å / Num. all: 45179 / Num. obs: 44298 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rsym value: 0.057 / Net I/σ(I): 23.62
Reflection shellResolution: 2.2→2.3 Å / Mean I/σ(I) obs: 3.09 / Rsym value: 0.648 / % possible all: 95.8

-
Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4OET

4oet


Resolution: 2.2→46.626 Å / SU ML: 0.31 / σ(F): 1.35 / Phase error: 27.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 2215 5 %Random
Rwork0.1923 ---
obs0.1947 44286 98.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→46.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8032 0 66 307 8405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078309
X-RAY DIFFRACTIONf_angle_d0.88411224
X-RAY DIFFRACTIONf_dihedral_angle_d12.753054
X-RAY DIFFRACTIONf_chiral_restr0.0391188
X-RAY DIFFRACTIONf_plane_restr0.0041436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.2480.40891300.33682476X-RAY DIFFRACTION94
2.248-2.30030.30491380.27282618X-RAY DIFFRACTION98
2.3003-2.35780.29751370.25182598X-RAY DIFFRACTION98
2.3578-2.42150.30481370.24892611X-RAY DIFFRACTION98
2.4215-2.49280.36031370.25072599X-RAY DIFFRACTION98
2.4928-2.57320.32671380.23342617X-RAY DIFFRACTION98
2.5732-2.66520.27881390.23382641X-RAY DIFFRACTION98
2.6652-2.77190.30991360.22152588X-RAY DIFFRACTION98
2.7719-2.8980.26311390.21262639X-RAY DIFFRACTION99
2.898-3.05080.28211390.2232637X-RAY DIFFRACTION98
3.0508-3.24190.22251370.21252615X-RAY DIFFRACTION99
3.2419-3.49210.23061400.19662648X-RAY DIFFRACTION99
3.4921-3.84340.2271400.16462668X-RAY DIFFRACTION99
3.8434-4.39920.18991400.15052663X-RAY DIFFRACTION99
4.3992-5.54110.18211420.15912690X-RAY DIFFRACTION99
5.5411-46.63640.23311460.17012763X-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)
12.1194-0.1624-0.36234.6067-0.96943.02550.10010.04230.1814-0.0482-0.07180.3607-0.20270.1352-0.04040.2518-0.0254-0.07060.2376-0.02120.3181-57.687528.0337-6.8166
24.126-3.2169-1.67969.18072.96562.75740.13620.64130.1354-0.8769-0.1513-0.5575-0.0930.2475-0.03290.3752-0.07960.05340.5919-0.00830.324-40.935823.212-16.8149
31.41990.63510.16893.49240.63221.685-0.05860.019-0.0380.09090.088-0.05250.270.29120.00050.27150.0907-0.03770.32610.01910.2105-54.61160.1032-6.6435
41.5963-0.1559-0.63282.05860.92272.0322-0.3178-0.1491-0.44130.11120.21340.03320.49240.31490.09370.43950.1360.07950.3087-0.01130.4513-72.9418-29.750133.1529
51.45160.1512-0.24281.44180.36822.4696-0.1714-0.6876-0.26210.54630.1498-0.11820.50110.6018-0.00070.56130.24860.05240.6940.02930.4817-71.523-20.195653.3032
60.9708-0.4954-1.2983.43391.2112.31440.5786-0.38350.8624-0.38830.2143-0.0678-1.06180.7001-0.55290.73-0.16890.29750.4764-0.18090.8093-73.65289.168637.2178
72.3516-0.2525-0.79232.44040.59212.49740.0542-0.20540.2106-0.11020.1754-0.1083-0.1510.5793-0.14810.2511-0.01230.04640.3345-0.08240.289-71.8507-8.920435.3472
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 178 )
2X-RAY DIFFRACTION2chain 'B' and (resid 179 through 208 )
3X-RAY DIFFRACTION3chain 'B' and (resid 209 through 494 )
4X-RAY DIFFRACTION4chain 'A' and (resid 2 through 151 )
5X-RAY DIFFRACTION5chain 'A' and (resid 152 through 246 )
6X-RAY DIFFRACTION6chain 'A' and (resid 247 through 357 )
7X-RAY DIFFRACTION7chain 'A' and (resid 358 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