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- PDB-5z6v: Crystal structure of a substrate-binding protein from Rhodothermu... -

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Basic information

Entry
Database: PDB / ID: 5z6v
TitleCrystal structure of a substrate-binding protein from Rhodothermus marinus
ComponentsABC-type uncharacterized transport system periplasmic component-like protein
KeywordsPROTEIN TRANSPORT / substrate binding protein / SBP
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 / SAD / Resolution: 1.87 Å
AuthorsBae, J.E. / Kim, I.J. / Nam, K.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)2017R1D1A1B03033087 Korea, Republic Of
National Research Foundation (Korea)2017M3A9F6029736 Korea, Republic Of
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Crystal structure of a substrate-binding protein from Rhodothermus marinus reveals a single alpha / beta-domain.
Authors: Bae, J.E. / Kim, I.J. / Kim, K.J. / Nam, K.H.
History
DepositionJan 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)21,0381
Polymers21,0381
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7670 Å2
Unit cell
Length a, b, c (Å)63.900, 63.320, 34.666
Angle α, β, γ (deg.)90.00, 97.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-289-

HOH

21A-295-

HOH

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Components

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


Mass: 21037.615 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) / Strain (production host): BL21(DE3) / References: UniProt: D0MDR1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
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: 1.65 Å3/Da / Density % sol: 25.62 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: sodium acetate, MgCl2, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 10741 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.057 / Rrim(I) all: 0.145 / Net I/σ(I): 48.38
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.381 / Num. unique obs: 530 / Rpim(I) all: 0.15 / Rrim(I) all: 0.41 / % possible all: 97.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.87→44.8 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.581 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1984 523 4.9 %RANDOM
Rwork0.15377 ---
obs0.15596 10218 94.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.125 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20.03 Å2
2--0.16 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.87→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 0 96 1313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191238
X-RAY DIFFRACTIONr_bond_other_d0.0030.021219
X-RAY DIFFRACTIONr_angle_refined_deg2.031.9681681
X-RAY DIFFRACTIONr_angle_other_deg1.13932813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2755157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.00924.31451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3415208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.627159
X-RAY DIFFRACTIONr_chiral_restr0.1320.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211364
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02241
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2821.011631
X-RAY DIFFRACTIONr_mcbond_other1.2721.008630
X-RAY DIFFRACTIONr_mcangle_it2.0051.505787
X-RAY DIFFRACTIONr_mcangle_other2.0061.507788
X-RAY DIFFRACTIONr_scbond_it2.8851.462607
X-RAY DIFFRACTIONr_scbond_other2.8841.464608
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3942.013895
X-RAY DIFFRACTIONr_long_range_B_refined6.53513.8111374
X-RAY DIFFRACTIONr_long_range_B_other6.34513.6391360
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.874→1.923 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.189 26 -
Rwork0.165 438 -
obs--56.52 %

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