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- PDB-6k1w: Crystal structure of Rhodothermus marinus substrate-binding prote... -

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Basic information

Entry
Database: PDB / ID: 6k1w
TitleCrystal structure of Rhodothermus marinus substrate-binding protein at pH 5.5
ComponentsABC-type uncharacterized transport system periplasmic component-like protein
KeywordsTRANSPORT PROTEIN / substrate binding protein / SBP / substrate binding domain
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2017R1D1A1B03033087 Korea, Republic Of
National Research Foundation (Korea)NRF-2017M3A9F6029736 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of Rhodothermus marinus substrate-binding protein at pH 5.5
Authors: Nam, K.H.
History
DepositionMay 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)18,3941
Polymers18,3941
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.421, 48.613, 58.111
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ABC-type uncharacterized transport system periplasmic component-like protein


Mass: 18394.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10) (bacteria)
Strain: ATCC 43812 / DSM 4252 / R-10 / 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.: 140 / Source method: isolated from a natural source / Formula: H2O

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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: 1.78 Å3/Da / Density % sol: 30.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: Magnesium chloride, BIS-Tris, PEG 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: 0.9796 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.5→39.29 Å / Num. obs: 21337 / % possible obs: 97.7 % / Redundancy: 5.4 % / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.031 / Rrim(I) all: 0.073 / Net I/σ(I): 40.125
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 5.57 / Num. unique obs: 1064 / CC1/2: 0.888 / Rpim(I) all: 0.17 / Rrim(I) all: 0.39 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z6V

5z6v


Resolution: 1.5→37.29 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.403 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.088
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 2007 9.5 %RANDOM
Rwork0.1855 ---
obs0.1887 19186 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.55 Å2 / Biso mean: 22.614 Å2 / Biso min: 9.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.5→37.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1151 0 0 140 1291
Biso mean---36.67 -
Num. residues----149
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 159 -
Rwork0.234 1407 -
all-1566 -
obs--99.3 %

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