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- PDB-7s6g: Crystal structure of PhnD from Synechococcus MITS9220 in complex ... -

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Basic information

Entry
Database: PDB / ID: 7s6g
TitleCrystal structure of PhnD from Synechococcus MITS9220 in complex with phosphate
ComponentsPhosphonate ABC type transporter/ substrate binding component
KeywordsTRANSPORT PROTEIN / Substrate-binding protein / marine cyanobacteria / phosphate-binding protein
Function / homologyPutative ABC transporter periplasmic binding protein PhnD-like / Phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein / ATP-binding cassette (ABC) transporter complex / transmembrane transport / PHOSPHATE ION / Phosphonate ABC type transporter/ substrate binding component
Function and homology information
Biological speciesSynechococcus sp. MIT S9220 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.02 Å
AuthorsShah, B.S. / Mikolajek, H. / Orr, C.M. / Mykhaylyk, V. / Owens, R.J. / Paulsen, I.T.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP200102944 Australia
Australian Research Council (ARC)CE200100029 Australia
CitationJournal: Isme J / Year: 2023
Title: Marine picocyanobacterial PhnD1 shows specificity for various phosphorus sources but likely represents a constitutive inorganic phosphate transporter.
Authors: Shah, B.S. / Ford, B.A. / Varkey, D. / Mikolajek, H. / Orr, C. / Mykhaylyk, V. / Owens, R.J. / Paulsen, I.T.
History
DepositionSep 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphonate ABC type transporter/ substrate binding component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,78915
Polymers30,1531
Non-polymers63614
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.590, 40.670, 106.680
Angle α, β, γ (deg.)90.000, 92.130, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-433-

HOH

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Components

#1: Protein Phosphonate ABC type transporter/ substrate binding component


Mass: 30153.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. MIT S9220 (bacteria) / Gene: SynMITS9220_01173 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Lemo21 / References: UniProt: A0A7G8IVX7
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 25 % PEG 3350, 30 % Ethylene Glycol

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Data collection

DiffractionMean temperature: 50 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 3.09960, 2.7552, 4.8621, 5.1660
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Feb 28, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
13.09961
22.75521
34.86211
45.1661
ReflectionResolution: 1.8→106.606 Å / Num. obs: 18073 / % possible obs: 69.8 % / Redundancy: 10.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.027 / Rrim(I) all: 0.068 / Net I/σ(I): 17.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.99-101.2120.032280.9990.0120.033
1.8-1.845.10.5813080.9390.4080.714

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.02→106.606 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.198 / WRfactor Rwork: 0.172 / SU B: 2.933 / SU ML: 0.082 / Average fsc free: 0.9601 / Average fsc work: 0.9673 / Cross valid method: FREE R-VALUE / ESU R: 0.179 / ESU R Free: 0.136
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1763 931 5.151 %
Rwork0.1528 17142 -
all0.154 --
obs-18073 99.291 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.19 Å2
Baniso -1Baniso -2Baniso -3
1-1.602 Å2-0 Å2-0.925 Å2
2--0.004 Å2-0 Å2
3----1.533 Å2
Refinement stepCycle: LAST / Resolution: 2.02→106.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2129 0 27 256 2412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132188
X-RAY DIFFRACTIONr_bond_other_d0.0010.0142119
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.652959
X-RAY DIFFRACTIONr_angle_other_deg1.4481.5794850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0245274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.08820.083120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3815359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6891523
X-RAY DIFFRACTIONr_chiral_restr0.0870.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022492
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02546
X-RAY DIFFRACTIONr_nbd_refined0.2120.2425
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.21966
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21082
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21042
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2203
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.080.23
X-RAY DIFFRACTIONr_nbd_other0.1840.224
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2360.213
X-RAY DIFFRACTIONr_mcbond_it1.8011.7051099
X-RAY DIFFRACTIONr_mcbond_other1.7991.7011098
X-RAY DIFFRACTIONr_mcangle_it2.5532.5421372
X-RAY DIFFRACTIONr_mcangle_other2.5542.5461373
X-RAY DIFFRACTIONr_scbond_it2.9992.0741089
X-RAY DIFFRACTIONr_scbond_other2.9982.0781090
X-RAY DIFFRACTIONr_scangle_it4.6492.9391587
X-RAY DIFFRACTIONr_scangle_other4.6482.9441588
X-RAY DIFFRACTIONr_lrange_it6.39621.5632519
X-RAY DIFFRACTIONr_lrange_other6.27320.9882459
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.02-2.0720.198470.17211730.17313440.940.95290.77380.162
2.072-2.1290.208750.15812230.1612980.9410.961000.156
2.129-2.190.174740.14311800.14412540.9620.9691000.143
2.19-2.2580.194630.14811720.1512350.9390.9551000.148
2.258-2.3320.173600.13911280.1411880.9610.9661000.145
2.332-2.4140.159480.12310890.12411370.9730.9781000.13
2.414-2.5050.173650.13510700.13711350.9630.9721000.139
2.505-2.6070.159550.1479850.14710400.9670.9651000.158
2.607-2.7230.22590.15110100.15510690.9410.9631000.164
2.723-2.8560.172490.1579270.1589760.9640.9691000.171
2.856-3.010.142460.1458710.1459170.9650.9731000.166
3.01-3.1920.192450.1658600.1669050.9630.9681000.186
3.192-3.4130.205340.1638090.1658430.9540.9611000.182
3.413-3.6860.234300.1787520.187820.9490.9611000.204
3.686-4.0370.179310.1496870.157180.9720.9731000.182
4.037-4.5130.143540.1346010.1346550.9810.9811000.173
4.513-5.2090.189330.1415470.1445800.9760.9811000.183
5.209-6.3760.145140.1914930.195070.9830.9781000.241
6.376-9.0010.142330.1643480.1623810.9810.9811000.215
9.001-106.6060.15160.1652160.1642320.9830.9741000.222

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