[English] 日本語
Yorodumi
- PDB-4oxr: Structure of Staphylococcus pseudintermedius metal-binding protei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4oxr
TitleStructure of Staphylococcus pseudintermedius metal-binding protein SitA in complex with Manganese
ComponentsManganese ABC transporter, periplasmic-binding protein SitA
KeywordsMETAL BINDING PROTEIN / Manganese binding protein / SBP / ABC transporter
Function / homologyNitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / : / :
Function and homology information
Biological speciesStaphylococcus pseudintermedius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAbate, F. / Malito, E. / Bottomley, M.
CitationJournal: Biosci.Rep. / Year: 2014
Title: Apo, Zn2+-bound and Mn2+-bound structures reveal ligand-binding properties of SitA from the pathogen Staphylococcus pseudintermedius.
Authors: Abate, F. / Malito, E. / Cozzi, R. / Lo Surdo, P. / Maione, D. / Bottomley, M.J.
History
DepositionFeb 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Feb 11, 2015Group: Database references
Revision 1.4Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / software / struct_keywords / struct_site / symmetry
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text / _struct_site.details / _symmetry.Int_Tables_number
Revision 1.5Sep 27, 2023Group: 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 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Manganese ABC transporter, periplasmic-binding protein SitA
B: Manganese ABC transporter, periplasmic-binding protein SitA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4844
Polymers64,3742
Non-polymers1102
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-5 kcal/mol
Surface area25140 Å2
2
A: Manganese ABC transporter, periplasmic-binding protein SitA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2422
Polymers32,1871
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Manganese ABC transporter, periplasmic-binding protein SitA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2422
Polymers32,1871
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.580, 57.490, 112.349
Angle α, β, γ (deg.)90.00, 101.95, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 29 - 306 / Label seq-ID: 8 - 285

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

-
Components

#1: Protein Manganese ABC transporter, periplasmic-binding protein SitA


Mass: 32187.090 Da / Num. of mol.: 2 / Fragment: ectodomain (UNP residues 23-306)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus pseudintermedius (bacteria)
Strain: IV369-1041 / Gene: SPSE_2131 / Plasmid: pET-15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F0P9H5
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1,1,1,3,3,3-hexafluoro-2-propanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2→46.45 Å / Num. obs: 33582 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 16.69 Å2 / Rsym value: 0.116 / Net I/σ(I): 11.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 4.7 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1593)refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PSZ

1psz


Resolution: 2→39.417 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2332 1701 5.07 %
Rwork0.183 --
obs0.1856 33559 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.8 Å2
Refinement stepCycle: LAST / Resolution: 2→39.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4423 0 2 181 4606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014528
X-RAY DIFFRACTIONf_angle_d1.4536096
X-RAY DIFFRACTIONf_dihedral_angle_d10.8741739
X-RAY DIFFRACTIONf_chiral_restr0.064662
X-RAY DIFFRACTIONf_plane_restr0.009784
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2497X-RAY DIFFRACTION6.633TORSIONAL
12B2497X-RAY DIFFRACTION6.633TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05890.34241460.24052614X-RAY DIFFRACTION97
2.0589-2.12530.2921680.22642599X-RAY DIFFRACTION98
2.1253-2.20130.28711250.21762645X-RAY DIFFRACTION98
2.2013-2.28940.25221490.21182617X-RAY DIFFRACTION98
2.2894-2.39360.26461190.212635X-RAY DIFFRACTION98
2.3936-2.51980.23871290.20472666X-RAY DIFFRACTION98
2.5198-2.67760.2971410.19622646X-RAY DIFFRACTION98
2.6776-2.88430.22231440.18842651X-RAY DIFFRACTION98
2.8843-3.17440.24311430.18962663X-RAY DIFFRACTION99
3.1744-3.63350.2171170.16382717X-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