[English] 日本語
Yorodumi
- PDB-8wxp: Crystal structure of substrate-binding protein from Rhodothermus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wxp
TitleCrystal structure of substrate-binding protein from Rhodothermus marinus (Dose IV)
ComponentsABC-type uncharacterized transport system periplasmic component-like protein
KeywordsPROTEIN TRANSPORT / substrate binding protein
Function / homologyABC transporter, substrate-binding protein / ABC transporter substrate binding protein / ABC-type uncharacterized transport system periplasmic component-like protein
Function and homology information
Biological speciesRhodothermus marinus DSM 4252 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029736 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2021R1I1A1A01050838 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2020M3H1A1075314 Korea, Republic Of
Citation
Journal: Data Brief / Year: 2024
Title: Data of radiation damage on selenomethionine-substituted single-domain substrate-binding protein.
Authors: Nam, K.H.
#1: Journal: Crystals / Year: 2023
Title: Radiation Damage on Selenomethionine-Substituted Single-Domain Substrate-Binding Protein.
Authors: Nam, K.H.
History
DepositionOct 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 22, 2024Group: Database references / Category: citation / citation_author

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ABC-type uncharacterized transport system periplasmic component-like protein
B: ABC-type uncharacterized transport system periplasmic component-like protein


Theoretical massNumber of molelcules
Total (without water)36,2432
Polymers36,2432
Non-polymers00
Water1,17165
1
A: ABC-type uncharacterized transport system periplasmic component-like protein


Theoretical massNumber of molelcules
Total (without water)18,1211
Polymers18,1211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC-type uncharacterized transport system periplasmic component-like protein


Theoretical massNumber of molelcules
Total (without water)18,1211
Polymers18,1211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.173, 64.136, 69.733
Angle α, β, γ (deg.)90.000, 96.110, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein ABC-type uncharacterized transport system periplasmic component-like protein


Mass: 18121.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodothermus marinus DSM 4252 (bacteria)
Gene: Rmar_2176 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0MDR1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, MgCl2, polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.75→39.06 Å / Num. obs: 54358 / % possible obs: 99.77 % / Redundancy: 6 % / Biso Wilson estimate: 23.47 Å2 / CC1/2: 0.997 / Net I/σ(I): 5.9
Reflection shellResolution: 1.75→1.81 Å / Num. unique obs: 2791 / CC1/2: 0.547

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→39.05 Å / SU ML: 0.2693 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.5734
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2703 3880 7.14 %
Rwork0.2233 50478 -
obs0.2265 54358 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.96 Å2
Refinement stepCycle: LAST / Resolution: 1.75→39.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 0 65 2473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612478
X-RAY DIFFRACTIONf_angle_d0.86073370
X-RAY DIFFRACTIONf_chiral_restr0.0573395
X-RAY DIFFRACTIONf_plane_restr0.0072434
X-RAY DIFFRACTIONf_dihedral_angle_d5.777337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.41381310.39461723X-RAY DIFFRACTION95.62
1.77-1.790.3561400.37131783X-RAY DIFFRACTION96.93
1.79-1.820.35851370.35351771X-RAY DIFFRACTION97.1
1.82-1.840.39131380.34091778X-RAY DIFFRACTION99.43
1.84-1.870.40141420.33131833X-RAY DIFFRACTION99.7
1.87-1.90.37031430.31081832X-RAY DIFFRACTION99.45
1.9-1.930.34051340.29251770X-RAY DIFFRACTION99.37
1.93-1.960.34231430.27641885X-RAY DIFFRACTION99.75
1.96-1.990.2821340.28291783X-RAY DIFFRACTION99.69
1.99-2.030.31591400.27341807X-RAY DIFFRACTION99.79
2.03-2.070.29261400.25711830X-RAY DIFFRACTION99.85
2.07-2.110.29221360.23591825X-RAY DIFFRACTION99.9
2.11-2.150.26391430.23951815X-RAY DIFFRACTION99.8
2.15-2.20.28511390.2231786X-RAY DIFFRACTION99.69
2.2-2.260.23681400.22831838X-RAY DIFFRACTION99.95
2.26-2.320.24061400.21081794X-RAY DIFFRACTION99.79
2.32-2.390.26471390.23221823X-RAY DIFFRACTION99.8
2.39-2.470.25971380.22151825X-RAY DIFFRACTION99.95
2.47-2.550.30221420.22961818X-RAY DIFFRACTION99.75
2.55-2.660.27761410.22531825X-RAY DIFFRACTION99.59
2.66-2.780.26591400.23031807X-RAY DIFFRACTION99.74
2.78-2.920.26221370.21341780X-RAY DIFFRACTION99.74
2.92-3.110.27131390.22311824X-RAY DIFFRACTION99.8
3.11-3.350.27011390.19771834X-RAY DIFFRACTION99.75
3.35-3.680.21021380.18021807X-RAY DIFFRACTION99.39
3.68-4.220.20071370.17621808X-RAY DIFFRACTION98.48
4.22-5.310.27211410.17711798X-RAY DIFFRACTION98.58
5.31-39.050.2591290.21311676X-RAY DIFFRACTION92.33

+
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://pdbjlc1.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