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

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Basic information

Entry
Database: PDB / ID: 8wxn
TitleCrystal structure of substrate-binding protein from Rhodothermus marinus (Dose II)
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: 1.58 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 23, 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
Water1,946108
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)63.552, 64.164, 69.863
Angle α, β, γ (deg.)90.000, 96.070, 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.: 108 / 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: 1.96 Å3/Da / Density % sol: 37.22 %
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: 1.58→36.56 Å / Num. obs: 74744 / % possible obs: 99.75 % / Redundancy: 6 % / Biso Wilson estimate: 20.48 Å2 / CC1/2: 0.997 / Net I/σ(I): 7
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 6 % / Num. unique obs: 3822 / CC1/2: 0.656 / % possible all: 100

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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: 1.58→36.55 Å / SU ML: 0.2619 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.1841
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.259 3917 5.24 %
Rwork0.2216 70827 -
obs0.2235 74744 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.21 Å2
Refinement stepCycle: LAST / Resolution: 1.58→36.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 0 108 2516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092478
X-RAY DIFFRACTIONf_angle_d0.96993370
X-RAY DIFFRACTIONf_chiral_restr0.0616395
X-RAY DIFFRACTIONf_plane_restr0.0095434
X-RAY DIFFRACTIONf_dihedral_angle_d5.872337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60.45651390.40532561X-RAY DIFFRACTION99.01
1.6-1.620.37391440.37162561X-RAY DIFFRACTION99.56
1.62-1.640.39971390.36972492X-RAY DIFFRACTION99.36
1.64-1.660.39121400.34832570X-RAY DIFFRACTION99.74
1.66-1.690.3711410.34892521X-RAY DIFFRACTION99.48
1.69-1.710.35191400.33752523X-RAY DIFFRACTION99.85
1.71-1.740.34791420.32932570X-RAY DIFFRACTION99.56
1.74-1.770.40061400.31362476X-RAY DIFFRACTION99.73
1.77-1.80.31341400.28012557X-RAY DIFFRACTION99.67
1.8-1.830.25731430.26612534X-RAY DIFFRACTION99.78
1.83-1.870.26931440.26522582X-RAY DIFFRACTION99.82
1.87-1.90.31591370.25582498X-RAY DIFFRACTION99.77
1.9-1.950.24621420.24652552X-RAY DIFFRACTION99.56
1.95-1.990.27191340.24132535X-RAY DIFFRACTION99.85
1.99-2.040.3111420.25462529X-RAY DIFFRACTION99.85
2.04-2.10.31021410.22612525X-RAY DIFFRACTION99.96
2.1-2.160.25911430.21022609X-RAY DIFFRACTION99.89
2.16-2.230.21321380.20812483X-RAY DIFFRACTION99.77
2.23-2.310.25651420.20912540X-RAY DIFFRACTION99.81
2.31-2.40.21521410.21472534X-RAY DIFFRACTION99.63
2.4-2.510.25471390.21982579X-RAY DIFFRACTION99.89
2.51-2.640.24871400.22452530X-RAY DIFFRACTION99.52
2.64-2.810.23561400.22352526X-RAY DIFFRACTION99.4
2.81-3.020.21211390.20442532X-RAY DIFFRACTION99.63
3.02-3.330.23661390.1992539X-RAY DIFFRACTION99.67
3.33-3.810.24651420.16762518X-RAY DIFFRACTION99.03
3.81-4.790.2041350.16692490X-RAY DIFFRACTION97.98
4.8-36.550.25541310.20442361X-RAY DIFFRACTION92.3

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