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- PDB-8wgk: Crystal structure of Rhodothermus marinus substrate-binding prote... -

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Basic information

Entry
Database: PDB / ID: 8wgk
TitleCrystal structure of Rhodothermus marinus substrate-binding protein (Br soaking)
ComponentsABC-type uncharacterized transport system periplasmic component-like protein
KeywordsTRANSPORT PROTEIN / 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, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021R1I1A1A01050838 Korea, Republic Of
CitationJournal: Biochem Biophys Rep / Year: 2024
Title: Structural and bioinformatics analysis of single-domain substrate-binding protein from Rhodothermus marinus.
Authors: Nam, K.H.
History
DepositionSep 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / citation_author
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.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,3901
Polymers20,3901
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.231, 49.129, 57.518
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ABC-type uncharacterized transport system periplasmic component-like protein / single domain substrate binding protein


Mass: 20389.668 Da / Num. of mol.: 1
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.: 51 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.6 Å3/Da / Density % sol: 23.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES , Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 13670 / % possible obs: 97.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 36.47
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.355 / Num. unique obs: 681

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→21.87 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2608 1341 10.02 %
Rwork0.2223 --
obs0.226 13384 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→21.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 0 51 1111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061077
X-RAY DIFFRACTIONf_angle_d0.8381460
X-RAY DIFFRACTIONf_dihedral_angle_d5.932143
X-RAY DIFFRACTIONf_chiral_restr0.055175
X-RAY DIFFRACTIONf_plane_restr0.008182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.810.24061330.22541213X-RAY DIFFRACTION100
1.81-1.890.26181340.2211210X-RAY DIFFRACTION100
1.89-1.970.23941360.20891210X-RAY DIFFRACTION100
1.97-2.070.2481320.20961200X-RAY DIFFRACTION100
2.07-2.20.27181420.2031225X-RAY DIFFRACTION100
2.2-2.370.25211350.2141216X-RAY DIFFRACTION99
2.37-2.610.25681320.2261231X-RAY DIFFRACTION99
2.61-2.990.24881370.22891219X-RAY DIFFRACTION99
2.99-3.760.26371410.21631229X-RAY DIFFRACTION98
3.77-21.870.27761190.23751090X-RAY DIFFRACTION82

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