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

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Basic information

Entry
Database: PDB / ID: 8wgl
TitleCrystal structure of Rhodothermus marinus substrate-binding protein (Hg 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: 2.3 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
B: ABC-type uncharacterized transport system periplasmic component-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1814
Polymers40,7792
Non-polymers4012
Water1,29772
1
A: ABC-type uncharacterized transport system periplasmic component-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5902
Polymers20,3901
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-27 kcal/mol
Surface area7570 Å2
MethodPISA
2
B: ABC-type uncharacterized transport system periplasmic component-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5902
Polymers20,3901
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-27 kcal/mol
Surface area7550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.645, 45.209, 57.041
Angle α, β, γ (deg.)90.00, 91.72, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 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: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.57 Å3/Da / Density % sol: 21.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Bis-Tris, pH 6.5, Magnesium chloride and 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: 2.3→50 Å / Num. obs: 11062 / % possible obs: 96.4 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.83
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.373 / Num. unique obs: 570 / % possible all: 100

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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: 2.3→24.11 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 1100 9.98 %
Rwork0.1915 --
obs0.1973 11017 96.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→24.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 2 72 2482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032450
X-RAY DIFFRACTIONf_angle_d0.6633328
X-RAY DIFFRACTIONf_dihedral_angle_d5.306330
X-RAY DIFFRACTIONf_chiral_restr0.044392
X-RAY DIFFRACTIONf_plane_restr0.006426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40.31651400.23861264X-RAY DIFFRACTION99
2.41-2.530.27571380.22731270X-RAY DIFFRACTION99
2.53-2.690.30191440.21891251X-RAY DIFFRACTION99
2.69-2.90.29311360.22021267X-RAY DIFFRACTION98
2.9-3.190.25971370.2041250X-RAY DIFFRACTION98
3.19-3.650.24351410.18211235X-RAY DIFFRACTION97
3.65-4.590.2081260.16561158X-RAY DIFFRACTION89
4.59-24.110.22511380.17081222X-RAY DIFFRACTION92

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