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

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Basic information

Entry
Database: PDB / ID: 8wxp
TitleCrystal structure of substrate-binding protein from Rhodothermus marinus (Dose IV)
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: 1.75 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 1.3Nov 13, 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
Water1,17165
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)63.173, 64.136, 69.733
Angle α, β, γ (deg.)90.000, 96.110, 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.: 65 / 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: 1.94 Å3/Da / Density % sol: 36.69 %
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: 1.75→39.06 Å / Num. obs: 54358 / % possible obs: 99.77 % / Redundancy: 6 % / Biso Wilson estimate: 23.47 Å2 / CC1/2: 0.997 / Net I/σ(I): 5.9
Reflection shellResolution: 1.75→1.81 Å / Num. unique obs: 2791 / CC1/2: 0.547

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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: 1.75→39.05 Å / SU ML: 0.2693 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.5734
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2703 3880 7.14 %
Rwork0.2233 50478 -
obs0.2265 54358 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.96 Å2
Refinement stepCycle: LAST / Resolution: 1.75→39.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 0 65 2473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612478
X-RAY DIFFRACTIONf_angle_d0.86073370
X-RAY DIFFRACTIONf_chiral_restr0.0573395
X-RAY DIFFRACTIONf_plane_restr0.0072434
X-RAY DIFFRACTIONf_dihedral_angle_d5.777337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.41381310.39461723X-RAY DIFFRACTION95.62
1.77-1.790.3561400.37131783X-RAY DIFFRACTION96.93
1.79-1.820.35851370.35351771X-RAY DIFFRACTION97.1
1.82-1.840.39131380.34091778X-RAY DIFFRACTION99.43
1.84-1.870.40141420.33131833X-RAY DIFFRACTION99.7
1.87-1.90.37031430.31081832X-RAY DIFFRACTION99.45
1.9-1.930.34051340.29251770X-RAY DIFFRACTION99.37
1.93-1.960.34231430.27641885X-RAY DIFFRACTION99.75
1.96-1.990.2821340.28291783X-RAY DIFFRACTION99.69
1.99-2.030.31591400.27341807X-RAY DIFFRACTION99.79
2.03-2.070.29261400.25711830X-RAY DIFFRACTION99.85
2.07-2.110.29221360.23591825X-RAY DIFFRACTION99.9
2.11-2.150.26391430.23951815X-RAY DIFFRACTION99.8
2.15-2.20.28511390.2231786X-RAY DIFFRACTION99.69
2.2-2.260.23681400.22831838X-RAY DIFFRACTION99.95
2.26-2.320.24061400.21081794X-RAY DIFFRACTION99.79
2.32-2.390.26471390.23221823X-RAY DIFFRACTION99.8
2.39-2.470.25971380.22151825X-RAY DIFFRACTION99.95
2.47-2.550.30221420.22961818X-RAY DIFFRACTION99.75
2.55-2.660.27761410.22531825X-RAY DIFFRACTION99.59
2.66-2.780.26591400.23031807X-RAY DIFFRACTION99.74
2.78-2.920.26221370.21341780X-RAY DIFFRACTION99.74
2.92-3.110.27131390.22311824X-RAY DIFFRACTION99.8
3.11-3.350.27011390.19771834X-RAY DIFFRACTION99.75
3.35-3.680.21021380.18021807X-RAY DIFFRACTION99.39
3.68-4.220.20071370.17621808X-RAY DIFFRACTION98.48
4.22-5.310.27211410.17711798X-RAY DIFFRACTION98.58
5.31-39.050.2591290.21311676X-RAY DIFFRACTION92.33

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