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- PDB-8jv1: Structure of the SAR11 PotD in complex with GABA -

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Basic information

Entry
Database: PDB / ID: 8jv1
TitleStructure of the SAR11 PotD in complex with GABA
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 / GAMMA-AMINO-BUTANOIC ACID / Spermidine/putrescine-binding periplasmic protein
Function and homology information
Biological speciesPelagibacter sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.309 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 GABA
Authors: Ma, Q. / Liu, C.
History
DepositionJun 27, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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)40,3508
Polymers39,4431
Non-polymers9077
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.005, 78.348, 79.725
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 , 6 types, 430 molecules

#2: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H9NO2 / 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: isolated from a natural source / 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 55.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The protein in complex with GABA was crystallized in drops containing 1 ul protein solution (60 mg/ml protein in buffer containing 10 mM HEPES, 150 mM NaCl, 50 mM GABA, pH 7.5) and 1 ul ...Details: The protein in complex with GABA was crystallized in drops containing 1 ul protein solution (60 mg/ml protein in buffer containing 10 mM HEPES, 150 mM NaCl, 50 mM GABA, 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: 1.309→55.881 Å / Num. obs: 105074 / % possible obs: 99.2 % / Redundancy: 12.3 % / CC1/2: 0.999 / Rpim(I) all: 0.014 / Rrim(I) all: 0.049 / Rsym value: 0.047 / Net I/σ(I): 25.8
Reflection shellResolution: 1.309→1.332 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4870 / CC1/2: 0.839 / Rpim(I) all: 0.248 / Rrim(I) all: 0.698 / Rsym value: 0.648 / % possible all: 92.8

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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: 1.309→27.94 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 11.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.138 5228 4.98 %random
Rwork0.1225 ---
obs0.1233 105053 99.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.309→27.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 57 423 3247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062907
X-RAY DIFFRACTIONf_angle_d1.013935
X-RAY DIFFRACTIONf_dihedral_angle_d15.0641061
X-RAY DIFFRACTIONf_chiral_restr0.081399
X-RAY DIFFRACTIONf_plane_restr0.007505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3092-1.32410.18761080.17453074X-RAY DIFFRACTION92
1.3241-1.33970.21681650.16353139X-RAY DIFFRACTION95
1.3397-1.3560.1621750.14673202X-RAY DIFFRACTION97
1.356-1.37320.18431810.13623246X-RAY DIFFRACTION97
1.3732-1.39120.17171750.12813205X-RAY DIFFRACTION98
1.3912-1.41030.14912010.11993265X-RAY DIFFRACTION99
1.4103-1.43040.13131980.11633288X-RAY DIFFRACTION99
1.4304-1.45180.1211780.10513339X-RAY DIFFRACTION100
1.4518-1.47450.12481530.10013296X-RAY DIFFRACTION100
1.4745-1.49860.12791850.09813317X-RAY DIFFRACTION100
1.4986-1.52450.14021860.09873296X-RAY DIFFRACTION100
1.5245-1.55220.13191550.0973361X-RAY DIFFRACTION100
1.5522-1.5820.13261800.09753311X-RAY DIFFRACTION100
1.582-1.61430.12361860.09733315X-RAY DIFFRACTION100
1.6143-1.64940.12841710.09623337X-RAY DIFFRACTION100
1.6494-1.68780.13671650.09373350X-RAY DIFFRACTION100
1.6878-1.730.12681520.09583342X-RAY DIFFRACTION100
1.73-1.77680.1211610.10393388X-RAY DIFFRACTION100
1.7768-1.8290.13261640.10693366X-RAY DIFFRACTION100
1.829-1.88810.12261810.11033337X-RAY DIFFRACTION100
1.8881-1.95550.14711620.11853347X-RAY DIFFRACTION100
1.9555-2.03380.14311620.11493373X-RAY DIFFRACTION100
2.0338-2.12630.13621740.11763380X-RAY DIFFRACTION100
2.1263-2.23840.12271660.11423378X-RAY DIFFRACTION100
2.2384-2.37860.12482070.11683334X-RAY DIFFRACTION100
2.3786-2.56210.13281760.12063391X-RAY DIFFRACTION100
2.5621-2.81970.1351710.12793412X-RAY DIFFRACTION100
2.8197-3.22720.15771830.14113410X-RAY DIFFRACTION100
3.2272-4.0640.14641910.14023448X-RAY DIFFRACTION100
4.064-27.940.13312160.1323578X-RAY DIFFRACTION100

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