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- PDB-7zck: Room temperature crystal structure of PhnD from Synechococcus MIT... -

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Basic information

Entry
Database: PDB / ID: 7zck
TitleRoom temperature crystal structure of PhnD from Synechococcus MITS9220 in complex with phosphate
ComponentsPhosphonate ABC type transporter/ substrate binding component
KeywordsTRANSPORT PROTEIN / Substrate-binding protein / marine cyanobacteria / urea-binding protein
Function / homologyPutative ABC transporter periplasmic binding protein PhnD-like / Phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein / ABC transporter, phosphonate, periplasmic substrate-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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMikolajek, H. / Shah, B.S. / Paulsen, I.T. / Sandy, J. / Sanchez-Weatherby, J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP200102944 Australia
Australian Research Council (ARC)CE200100029 Australia
CitationJournal: Iucrj / Year: 2023
Title: Protein-to-structure pipeline for ambient-temperature in situ crystallography at VMXi.
Authors: Mikolajek, H. / Sanchez-Weatherby, J. / Sandy, J. / Gildea, R.J. / Campeotto, I. / Cheruvara, H. / Clarke, J.D. / Foster, T. / Fujii, S. / Paulsen, I.T. / Shah, B.S. / Hough, M.A.
History
DepositionMar 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2May 31, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 19, 2023Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,56711
Polymers30,1531
Non-polymers41410
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-93 kcal/mol
Surface area11970 Å2
Unit cell
Length a, b, c (Å)65.027, 40.683, 106.513
Angle α, β, γ (deg.)90.00, 92.78, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-414-

HOH

21C-452-

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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris pH 8.5, 25 % PEG 3350

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: VMXi / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Dec 2, 2020
RadiationMonochromator: Multilayer monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→53.17 Å / Num. obs: 26032 / % possible obs: 99.78 % / Redundancy: 8.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Net I/σ(I): 14.4
Reflection shellResolution: 1.8→1.82 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.387 / Mean I/σ(I) obs: 1 / Num. unique obs: 1271 / CC1/2: 0.416 / % possible all: 97.02

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2.multiplexdata reduction
xia2.multiplexdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7S6G

7s6g


Resolution: 1.8→53.17 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.076 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19705 1332 5.1 %RANDOM
Rwork0.15131 ---
obs0.15352 24584 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.661 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.01 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.8→53.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2125 0 14 128 2267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132194
X-RAY DIFFRACTIONr_bond_other_d0.0010.0142122
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.6462977
X-RAY DIFFRACTIONr_angle_other_deg1.4641.5794854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4775278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.20619.918122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79415360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8331524
X-RAY DIFFRACTIONr_chiral_restr0.0850.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022524
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02556
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_it2.6672.9111109
X-RAY DIFFRACTIONr_mcbond_other2.6612.9081108
X-RAY DIFFRACTIONr_mcangle_it3.6444.351388
X-RAY DIFFRACTIONr_mcangle_other3.6454.3541389
X-RAY DIFFRACTIONr_scbond_it4.3473.4721085
X-RAY DIFFRACTIONr_scbond_other4.3533.4831082
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8874.9691584
X-RAY DIFFRACTIONr_long_range_B_refined8.52634.72429
X-RAY DIFFRACTIONr_long_range_B_other8.39534.4812411
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å
RfactorNum. reflection% reflection
Rfree0.289 110 -
Rwork0.289 1650 -
obs--90.96 %

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