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- PDB-8jv4: Structure of the SAR11 PotD in complex with DMSP -

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Basic information

Entry
Database: PDB / ID: 8jv4
TitleStructure of the SAR11 PotD in complex with DMSP
ComponentsSpermidine/putrescine-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / PotD / substrate binding protein / solute-binding protein / periplasmic binding protein / ABC transporter system receptor / osmolyte / compatible solute / betaine / DMSP / GABA / amino acid / SAR11 / Candidatus Pelagibacter sp. HTCC7211
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid / Spermidine/putrescine-binding periplasmic protein
Function and homology information
Biological speciesPelagibacter sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.445 Å
AuthorsMa, Q. / Liu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)xxxx China
CitationJournal: To Be Published
Title: Structure of the SAR11 PotD in complex with DMSP
Authors: Ma, Q. / Liu, C.
History
DepositionJun 27, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 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: Spermidine/putrescine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3487
Polymers39,4431
Non-polymers9056
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-1 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.160, 78.383, 79.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Spermidine/putrescine-binding periplasmic protein


Mass: 39442.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pelagibacter sp. (strain HTCC7211) (bacteria)
Gene: potD, PB7211_697 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / References: UniProt: B6BQH5

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Non-polymers , 5 types, 422 molecules

#2: Chemical ChemComp-DQY / 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid


Mass: 136.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The protein in complex with DMSP was crystallized in drops containing 1 ul protein solution (60 mg/ml protein in buffer containing 10 mM HEPES, 150 mM NaCl, 15 mM DMSP-Cl, pH 7.5) and 1 ul ...Details: The protein in complex with DMSP was crystallized in drops containing 1 ul protein solution (60 mg/ml protein in buffer containing 10 mM HEPES, 150 mM NaCl, 15 mM DMSP-Cl, pH 7.5) and 1 ul reservoir solution (100 mM MES pH 6.5, 18% w/v mPEG 550).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.445→55.8 Å / Num. obs: 77717 / % possible obs: 98.4 % / Redundancy: 11.6 % / CC1/2: 0.999 / Rpim(I) all: 0.015 / Rrim(I) all: 0.054 / Rsym value: 0.052 / Net I/σ(I): 23.3
Reflection shellResolution: 1.445→1.47 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3260 / CC1/2: 0.8 / Rpim(I) all: 0.207 / Rrim(I) all: 0.553 / Rsym value: 0.508 / % possible all: 83.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSJan 10, 2022 (BUILT 20220820)data reduction
Aimless0.5.29data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.445→26.295 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1468 3791 4.88 %random
Rwork0.1217 ---
obs0.123 77699 98.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.445→26.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 57 416 3240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072907
X-RAY DIFFRACTIONf_angle_d0.9253934
X-RAY DIFFRACTIONf_dihedral_angle_d13.2261060
X-RAY DIFFRACTIONf_chiral_restr0.081398
X-RAY DIFFRACTIONf_plane_restr0.007505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4454-1.46370.17851250.15272269X-RAY DIFFRACTION83
1.4637-1.4830.17751160.13832430X-RAY DIFFRACTION89
1.483-1.50330.14171080.1282633X-RAY DIFFRACTION94
1.5033-1.52470.17091270.1132639X-RAY DIFFRACTION96
1.5247-1.54750.13811510.10822654X-RAY DIFFRACTION98
1.5475-1.57170.13461370.10312736X-RAY DIFFRACTION99
1.5717-1.59740.14091250.10032733X-RAY DIFFRACTION99
1.5974-1.6250.12751140.09292756X-RAY DIFFRACTION100
1.625-1.65450.12681360.09692761X-RAY DIFFRACTION100
1.6545-1.68630.16241600.1162755X-RAY DIFFRACTION100
1.6863-1.72080.17091340.11492767X-RAY DIFFRACTION100
1.7208-1.75820.14011460.10662752X-RAY DIFFRACTION100
1.7582-1.79910.13281460.1082766X-RAY DIFFRACTION100
1.7991-1.8440.1531540.10652737X-RAY DIFFRACTION100
1.844-1.89390.12651470.10962771X-RAY DIFFRACTION100
1.8939-1.94960.15031470.11212767X-RAY DIFFRACTION100
1.9496-2.01250.1471400.12012766X-RAY DIFFRACTION100
2.0125-2.08440.15261370.11922777X-RAY DIFFRACTION100
2.0844-2.16780.12841460.11472772X-RAY DIFFRACTION100
2.1678-2.26640.13581330.11272799X-RAY DIFFRACTION100
2.2664-2.38580.13111250.11292805X-RAY DIFFRACTION100
2.3858-2.53520.13221650.1162787X-RAY DIFFRACTION100
2.5352-2.73080.14071620.12172782X-RAY DIFFRACTION100
2.7308-3.00520.17761460.1312811X-RAY DIFFRACTION100
3.0052-3.43930.14941550.14182831X-RAY DIFFRACTION100
3.4393-4.330.13821390.12982874X-RAY DIFFRACTION100
4.33-26.2950.16421700.12762978X-RAY DIFFRACTION100

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