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- PDB-8wxo: Crystal structure of substrate-binding protein from Rhodothermus ... -

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Basic information

Entry
Database: PDB / ID: 8wxo
TitleCrystal structure of substrate-binding protein from Rhodothermus marinus (Dose III)
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: 1.68 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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


Theoretical massNumber of molelcules
Total (without water)36,2432
Polymers36,2432
Non-polymers00
Water1,54986
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)63.341, 64.122, 69.757
Angle α, β, γ (deg.)90.000, 96.080, 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

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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.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.95 Å3/Da / Density % sol: 36.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, MgCl2, polyethylene glycol 3350

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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: 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: 1.68→39.09 Å / Num. obs: 61756 / % possible obs: 99.79 % / Redundancy: 6 % / Biso Wilson estimate: 22.31 Å2 / CC1/2: 0.996 / Net I/σ(I): 6.4
Reflection shellResolution: 1.68→1.74 Å / Num. unique obs: 3159 / CC1/2: 0.608

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→39.08 Å / SU ML: 0.2602 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.4118
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2565 3907 6.33 %
Rwork0.2176 57849 -
obs0.2201 61756 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.78 Å2
Refinement stepCycle: LAST / Resolution: 1.68→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 0 86 2494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01632478
X-RAY DIFFRACTIONf_angle_d1.45433370
X-RAY DIFFRACTIONf_chiral_restr0.0903395
X-RAY DIFFRACTIONf_plane_restr0.0132434
X-RAY DIFFRACTIONf_dihedral_angle_d6.0694337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.70.40151350.39532008X-RAY DIFFRACTION97.81
1.7-1.720.41961400.38612064X-RAY DIFFRACTION99.32
1.72-1.740.32721390.38382118X-RAY DIFFRACTION99.21
1.74-1.770.41321340.37021983X-RAY DIFFRACTION99.34
1.77-1.790.40971440.33472125X-RAY DIFFRACTION99.52
1.79-1.820.36891390.31842098X-RAY DIFFRACTION99.69
1.82-1.850.30691350.29612023X-RAY DIFFRACTION99.72
1.85-1.880.32971440.282128X-RAY DIFFRACTION99.74
1.88-1.910.34231300.25832045X-RAY DIFFRACTION99.59
1.91-1.950.27061480.25752137X-RAY DIFFRACTION99.52
1.95-1.980.2791360.25182017X-RAY DIFFRACTION99.72
1.98-2.020.31841440.25382090X-RAY DIFFRACTION99.91
2.02-2.070.29711410.24742084X-RAY DIFFRACTION99.69
2.07-2.120.28691450.22892079X-RAY DIFFRACTION100
2.12-2.170.23041370.21842065X-RAY DIFFRACTION99.77
2.17-2.230.34161430.21112081X-RAY DIFFRACTION99.87
2.23-2.290.25121370.21772069X-RAY DIFFRACTION99.95
2.29-2.370.29841440.20492132X-RAY DIFFRACTION99.61
2.37-2.450.24091380.23242015X-RAY DIFFRACTION100
2.45-2.550.30421350.21182076X-RAY DIFFRACTION99.73
2.55-2.670.23251430.22852114X-RAY DIFFRACTION99.69
2.67-2.810.27831420.21012062X-RAY DIFFRACTION99.41
2.81-2.980.2311410.20632065X-RAY DIFFRACTION99.37
2.98-3.210.23891410.19572092X-RAY DIFFRACTION99.69
3.21-3.540.22161390.18172052X-RAY DIFFRACTION99.77
3.54-4.050.17741400.16782067X-RAY DIFFRACTION98.97
4.05-5.10.18581380.16172032X-RAY DIFFRACTION98.41
5.1-39.080.27761350.21161928X-RAY DIFFRACTION92.39

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