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- PDB-6k1x: Crystal structure of Rhodothermus marinus substrate-binding prote... -

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Basic information

Entry
Database: PDB / ID: 6k1x
TitleCrystal structure of Rhodothermus marinus substrate-binding protein at pH 6.0
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: 1.802 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 6.0
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
Water1,62190
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)34.913, 35.725, 115.572
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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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.: 90 / 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: 2.12 Å3/Da / Density % sol: 37.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: Ammonium sulfate, MES

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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: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 12659 / % possible obs: 90.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.057 / Rrim(I) all: 0.132 / Net I/σ(I): 27.6
Reflection shellResolution: 1.8→1.8743 Å / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 1440 / CC1/2: 0.904 / Rpim(I) all: 0.198 / Rrim(I) all: 0.471 / % possible all: 95

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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: 1.802→14.941 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.34
RfactorNum. reflection% reflection
Rfree0.2204 1278 10.1 %
Rwork0.1903 --
obs0.1935 12659 90.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.31 Å2 / Biso mean: 23.4756 Å2 / Biso min: 10.18 Å2
Refinement stepCycle: final / Resolution: 1.802→14.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1195 0 0 90 1285
Biso mean---30.42 -
Num. residues----155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071223
X-RAY DIFFRACTIONf_angle_d0.8091659
X-RAY DIFFRACTIONf_chiral_restr0.059196
X-RAY DIFFRACTIONf_plane_restr0.006211
X-RAY DIFFRACTIONf_dihedral_angle_d9.962744
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8023-1.87430.26381460.20221294144095
1.8743-1.95940.23131470.19711288143595
1.9594-2.06250.21471400.17841298143894
2.0625-2.19130.22281460.17641279142593
2.1913-2.35990.22071420.18151280142293
2.3599-2.59630.23031430.19341268141192
2.5963-2.96940.26821470.19781275142291
2.9694-3.73150.2011380.19361253139188
3.7315-14.94170.19551290.19021146127576

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