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- PDB-8jv2: Structure of the SAR11 PotD in complex with proline -

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Basic information

Entry
Database: PDB / ID: 8jv2
TitleStructure of the SAR11 PotD in complex with proline
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 / PROLINE / Spermidine/putrescine-binding periplasmic protein
Function and homology information
Biological speciesPelagibacter sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 proline
Authors: Ma, Q. / Liu, C.
History
DepositionJun 27, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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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)40,3277
Polymers39,4431
Non-polymers8846
Water7,819434
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 area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.848, 78.160, 79.493
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, 440 molecules

#2: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2 / 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: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The protein in complex with L-proline was crystallized in drops containing 1 ul protein solution (60 mg/ml protein in buffer containing 10 mM HEPES, 150 mM NaCl, 50 mM L-proline, pH 7.5) and ...Details: The protein in complex with L-proline was crystallized in drops containing 1 ul protein solution (60 mg/ml protein in buffer containing 10 mM HEPES, 150 mM NaCl, 50 mM L-proline, pH 7.5) and 1 ul reservoir solution (100 mM MES pH 6.5, 20% 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: 1.3→55.733 Å / Num. obs: 104876 / % possible obs: 97.7 % / Redundancy: 12.4 % / CC1/2: 1 / Rpim(I) all: 0.011 / Rrim(I) all: 0.041 / Rsym value: 0.039 / Net I/σ(I): 31.9
Reflection shellResolution: 1.3→1.322 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4306 / CC1/2: 0.874 / Rpim(I) all: 0.157 / Rrim(I) all: 0.457 / Rsym value: 0.426 / % possible all: 81

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSJan 10, 2022, built on 20220820data reduction
Aimless0.5.29data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→26.235 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 10.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1339 5230 4.99 %random
Rwork0.1188 ---
obs0.1196 104858 97.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→26.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 57 434 3258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062929
X-RAY DIFFRACTIONf_angle_d0.9363970
X-RAY DIFFRACTIONf_dihedral_angle_d12.5971077
X-RAY DIFFRACTIONf_chiral_restr0.08404
X-RAY DIFFRACTIONf_plane_restr0.007509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.18211080.15492700X-RAY DIFFRACTION79
1.3148-1.33020.18511370.14052914X-RAY DIFFRACTION86
1.3302-1.34650.15871570.13043121X-RAY DIFFRACTION92
1.3465-1.36350.14331770.12033155X-RAY DIFFRACTION95
1.3635-1.38150.15811810.11493219X-RAY DIFFRACTION96
1.3815-1.40040.13381990.10543223X-RAY DIFFRACTION96
1.4004-1.42040.12912060.10273260X-RAY DIFFRACTION98
1.4204-1.44160.12761820.09923308X-RAY DIFFRACTION99
1.4416-1.46410.11081510.09323342X-RAY DIFFRACTION99
1.4641-1.48810.12041880.09193327X-RAY DIFFRACTION98
1.4881-1.51380.12751800.09033333X-RAY DIFFRACTION99
1.5138-1.54130.12041600.09183343X-RAY DIFFRACTION99
1.5413-1.57090.1352000.0913312X-RAY DIFFRACTION99
1.5709-1.6030.11591750.08873343X-RAY DIFFRACTION99
1.603-1.63780.11241690.08973354X-RAY DIFFRACTION99
1.6378-1.67590.13031690.08993339X-RAY DIFFRACTION99
1.6759-1.71780.11111570.09163419X-RAY DIFFRACTION99
1.7178-1.76430.13041610.13360X-RAY DIFFRACTION99
1.7643-1.81620.1141490.10253400X-RAY DIFFRACTION100
1.8162-1.87480.11661860.10383377X-RAY DIFFRACTION100
1.8748-1.94180.13351720.11253399X-RAY DIFFRACTION99
1.9418-2.01950.13451680.11233396X-RAY DIFFRACTION100
2.0195-2.11140.14431720.1173424X-RAY DIFFRACTION100
2.1114-2.22260.11861710.10963412X-RAY DIFFRACTION100
2.2226-2.36180.11732030.1133377X-RAY DIFFRACTION100
2.3618-2.5440.12921820.11693440X-RAY DIFFRACTION100
2.544-2.79980.13671720.12933466X-RAY DIFFRACTION100
2.7998-3.20430.16121850.13943456X-RAY DIFFRACTION100
3.2043-4.03470.12821950.13653484X-RAY DIFFRACTION100
4.0347-26.2350.14722180.13363625X-RAY DIFFRACTION100

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