[English] 日本語
Yorodumi
- PDB-4ofl: Crystal structure of YntA from Yersinia pestis in complex with Ni... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ofl
TitleCrystal structure of YntA from Yersinia pestis in complex with Ni(L-His)2
ComponentsExtracytoplasmic Nickel-Binding Protein YpYntA
KeywordsTRANSPORT PROTEIN / Nickel import / Periplasmic / 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 / outer membrane-bounded periplasmic space
Similarity search - Function
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
HISTIDINE / NICKEL (II) ION / Solute-binding protein / Solute-binding protein
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 15, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Extracytoplasmic Nickel-Binding Protein YpYntA
B: Extracytoplasmic Nickel-Binding Protein YpYntA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,7498
Polymers110,0072
Non-polymers7426
Water1,910106
1
A: Extracytoplasmic Nickel-Binding Protein YpYntA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3754
Polymers55,0041
Non-polymers3713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Extracytoplasmic Nickel-Binding Protein YpYntA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3754
Polymers55,0041
Non-polymers3713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.040, 213.830, 52.870
Angle α, β, γ (deg.)90.00, 102.72, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

-
Components

#1: Protein Extracytoplasmic Nickel-Binding Protein YpYntA / Putative substrate-binding periplasmic protein of ABC transporter / YpYntA


Mass: 55003.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: oppA4, y1231, YP_2461, YPO2660 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CJS8, UniProt: A0A2U2H355*PLUS
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H10N3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 29 % PEG 10K , 50 mM Tris pH 8.5, 1 M NaCl + NiCl2 + L-His, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.7→46.451 Å / Num. all: 27904 / Num. obs: 26613 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Rsym value: 0.085 / Net I/σ(I): 10.54
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.14 / Rsym value: 0.512 / % possible all: 94.7

-
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 3RY3

3ry3


Resolution: 2.7→46.451 Å / SU ML: 0.39 / σ(F): 1.37 / Phase error: 25.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 1331 5 %
Rwork0.1928 --
obs0.1948 26600 95.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→46.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7724 0 46 106 7876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097998
X-RAY DIFFRACTIONf_angle_d0.78310888
X-RAY DIFFRACTIONf_dihedral_angle_d12.7592848
X-RAY DIFFRACTIONf_chiral_restr0.0311160
X-RAY DIFFRACTIONf_plane_restr0.0041422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6999-2.79640.35181330.25722515X-RAY DIFFRACTION95
2.7964-2.90830.31461350.25152579X-RAY DIFFRACTION97
2.9083-3.04070.29891330.25472526X-RAY DIFFRACTION97
3.0407-3.20090.32451340.24212546X-RAY DIFFRACTION96
3.2009-3.40140.31241350.2142553X-RAY DIFFRACTION96
3.4014-3.6640.23911310.21032488X-RAY DIFFRACTION94
3.664-4.03250.20661340.17372558X-RAY DIFFRACTION97
4.0325-4.61560.17741330.1532518X-RAY DIFFRACTION95
4.6156-5.81330.18911310.16792489X-RAY DIFFRACTION94
5.8133-46.45820.20041320.17152497X-RAY DIFFRACTION93
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)
11.902-0.81561.02212.21360.26191.94870.23710.039-0.14190.2398-0.0041-0.4550.66660.4591-0.16520.67570.168-0.09720.3401-0.05170.497711.4150.705644.9806
22.3713-0.7389-1.04234.11852.60713.82080.29180.35890.2228-0.46050.2814-0.56440.55780.7816-0.56840.68230.1422-0.05980.3829-0.04010.496515.65340.329541.2867
31.71020.99430.51131.24080.16591.15490.1087-0.00120.11480.0034-0.16460.14630.10850.03270.04920.17640.04840.0070.2362-0.02090.192414.079829.006644.4543
42.36861.05931.23623.03540.48581.9226-0.07870.1868-0.2891-0.37860.03950.11740.42070.02730.01670.3011-0.04860.06430.244-0.01550.2625-0.261718.668638.4875
52.64390.49191.39463.2423-1.39262.7779-0.21520.51270.5241-0.5298-0.02230.0373-0.54380.37410.30830.7298-0.0290.01630.34660.07320.5842.560187.017526.892
61.76-0.48871.32641.93550.81914.4215-0.1730.66270.3028-0.6704-0.045-0.5812-0.57121.08470.2330.6804-0.03170.12130.55310.21250.52827.567486.763324.2907
70.56290.64480.37662.36331.18822.04080.0950.03510.2193-0.0828-0.0588-0.4462-0.16670.0191-0.01960.23480.04270.0250.25560.05660.46962.191558.901425.8296
81.88360.550.79723.00641.30612.28640.092-0.12890.38550.3517-0.0346-0.0456-0.27350.0486-0.09020.3516-0.0265-0.00630.231-0.02490.42972.840369.839541.2226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 115 )
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 152 )
3X-RAY DIFFRACTION3chain 'A' and (resid 153 through 455 )
4X-RAY DIFFRACTION4chain 'A' and (resid 456 through 498 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 115 )
6X-RAY DIFFRACTION6chain 'B' and (resid 116 through 152 )
7X-RAY DIFFRACTION7chain 'B' and (resid 153 through 455 )
8X-RAY DIFFRACTION8chain 'B' and (resid 456 through 498 )

+
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