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

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Basic information

Entry
Database: PDB / ID: 8wxm
TitleCrystal structure of substrate-binding protein from Rhodothermus marinus (Dose I)
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: 1.5 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 / 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.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Database references / Category: citation / citation_author
Revision 1.3Oct 30, 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
Water2,972165
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)63.577, 63.925, 69.698
Angle α, β, γ (deg.)90.000, 96.040, 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.: 165 / 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: 36.86 %
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: 1.5→39.09 Å / Num. obs: 85769 / % possible obs: 98.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 17.68 Å2 / CC1/2: 0.997 / Net I/σ(I): 7.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.5 % / Num. unique obs: 4052 / CC1/2: 0.587 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→39.07 Å / SU ML: 0.2274 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.5469
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2467 3902 4.55 %
Rwork0.2195 81867 -
obs0.2207 85769 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.47 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 0 165 2573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00892478
X-RAY DIFFRACTIONf_angle_d0.97993370
X-RAY DIFFRACTIONf_chiral_restr0.0653395
X-RAY DIFFRACTIONf_plane_restr0.0093434
X-RAY DIFFRACTIONf_dihedral_angle_d5.9063337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.35351180.37922432X-RAY DIFFRACTION84.24
1.52-1.540.37471280.36482707X-RAY DIFFRACTION90.11
1.54-1.560.42241350.33942866X-RAY DIFFRACTION94.55
1.56-1.580.36261410.33032884X-RAY DIFFRACTION99.18
1.58-1.60.3621440.31213037X-RAY DIFFRACTION99.81
1.6-1.630.33241390.30712934X-RAY DIFFRACTION99.61
1.63-1.650.32191410.28312971X-RAY DIFFRACTION99.62
1.65-1.680.33511410.28322999X-RAY DIFFRACTION99.62
1.68-1.710.30021400.27942943X-RAY DIFFRACTION99.9
1.71-1.740.30431450.27463008X-RAY DIFFRACTION99.72
1.74-1.770.28831390.26722938X-RAY DIFFRACTION99.9
1.77-1.810.25131450.24742994X-RAY DIFFRACTION99.84
1.81-1.850.25491380.25092918X-RAY DIFFRACTION99.71
1.85-1.890.26651450.24573046X-RAY DIFFRACTION99.87
1.89-1.940.24581400.24182962X-RAY DIFFRACTION99.58
1.94-1.990.30141400.22572941X-RAY DIFFRACTION99.61
1.99-2.050.28011440.22913059X-RAY DIFFRACTION99.78
2.05-2.110.3121340.21932896X-RAY DIFFRACTION99.87
2.11-2.190.24311430.2072987X-RAY DIFFRACTION99.75
2.19-2.280.27081430.20792957X-RAY DIFFRACTION99.84
2.28-2.380.25941420.21622991X-RAY DIFFRACTION99.3
2.38-2.510.25471440.21562974X-RAY DIFFRACTION99.62
2.51-2.660.28311440.23082939X-RAY DIFFRACTION98.85
2.66-2.870.2251400.20782937X-RAY DIFFRACTION99.07
2.87-3.160.23571390.20062962X-RAY DIFFRACTION99.49
3.16-3.610.21011400.1752933X-RAY DIFFRACTION99.19
3.61-4.550.17591430.16492932X-RAY DIFFRACTION97.65
4.55-39.070.16351270.22720X-RAY DIFFRACTION91.19

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