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- PDB-7ug8: Crystal structure of a solute receptor from Synechococcus CC9311 ... -

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Basic information

Entry
Database: PDB / ID: 7ug8
TitleCrystal structure of a solute receptor from Synechococcus CC9311 in complex with alpha-ketovaleric and calcium
ComponentsKetoacid-binding protein
KeywordsTRANSPORT PROTEIN / Substrate-binding protein / marine cyanobacteria / ketoacid-binding protein
Function / homology
Function and homology information


organic acid transport / tripartite ATP-independent periplasmic transporter complex / organic acid binding / transmembrane transport / periplasmic space / metal ion binding
Similarity search - Function
Alpha-keto acid binding periplasmic protein / Solute binding protein, TakP-like / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
2-oxopentanoic acid / Extracytoplasmic solute receptor protein
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.796 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: To Be Published
Title: Crystal structure of a solute receptor from Synechococcus CC9311 in complex with alpha-ketovaleric and calcium
Authors: Shah, B.S. / Mikolajek, H. / Orr, C.M. / Mykhaylyk, V. / Owens, R. / Paulsen, I.T.
History
DepositionMar 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ketoacid-binding protein
B: Ketoacid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3578
Polymers76,9212
Non-polymers4376
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-32 kcal/mol
Surface area23750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.680, 54.750, 61.150
Angle α, β, γ (deg.)69.649, 77.732, 67.267
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 7 - 334 / Label seq-ID: 7 - 334

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Ketoacid-binding protein


Mass: 38460.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (strain CC9311) (bacteria)
Strain: CC9311 / Gene: sync_2776 / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo 21 (DE3) / References: UniProt: Q0I6F8
#2: Chemical ChemComp-69O / 2-oxopentanoic acid / 2-Ketopentanoic acid


Mass: 116.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.05 Å3/Da / Density % sol: 39.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02 M Sodium/Potassium Phosphate, 0.1M Bis Tris propane 7.5, 20% Peg 3350 Cryo: 30 % Peg 400

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Data collection

DiffractionMean temperature: 50 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.7552, 3.1790, 3.4925, 4.7686
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
12.75521
23.1791
33.49251
44.76861
Reflection

Entry-ID: 7UG8

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
1.796-50.2775076290.913.60.9990.0680.0240.073116.8
2.07-50.0813208475.74.70.998217.3
2.28-50.159535973.34.70.997319.1
3.5-57.163166181.950.99414
Reflection shellResolution: 9.06→50.23 Å / Redundancy: 23.3 % / Rmerge(I) obs: 0.039 / Num. unique obs: 451 / CC1/2: 0.999 / Rpim(I) all: 0.012 / Rrim(I) all: 0.041

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.796→50.277 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 3.728 / SU ML: 0.103 / Cross valid method: FREE R-VALUE / ESU R: 0.146 / ESU R Free: 0.121
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1898 2454 4.834 %
Rwork0.1687 48308 -
all0.17 --
obs-50762 89.014 %
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: 44.394 Å2
Baniso -1Baniso -2Baniso -3
1-2.341 Å2-1.224 Å2-0.948 Å2
2---1.642 Å21.715 Å2
3----0.183 Å2
Refinement stepCycle: LAST / Resolution: 1.796→50.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5159 0 26 255 5440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135356
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155010
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.6437258
X-RAY DIFFRACTIONr_angle_other_deg1.3751.57811483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73921.391302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10915851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8011543
X-RAY DIFFRACTIONr_chiral_restr0.0810.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026219
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021359
X-RAY DIFFRACTIONr_nbd_refined0.2010.21070
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.24380
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22576
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22276
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2214
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1110.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1080.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1290.213
X-RAY DIFFRACTIONr_nbd_other0.2050.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2630.26
X-RAY DIFFRACTIONr_mcbond_it3.8734.3772650
X-RAY DIFFRACTIONr_mcbond_other3.8674.3752649
X-RAY DIFFRACTIONr_mcangle_it5.0086.5393314
X-RAY DIFFRACTIONr_mcangle_other5.0086.5423315
X-RAY DIFFRACTIONr_scbond_it4.7534.8522706
X-RAY DIFFRACTIONr_scbond_other4.7484.852703
X-RAY DIFFRACTIONr_scangle_it6.797.0663941
X-RAY DIFFRACTIONr_scangle_other6.797.0663942
X-RAY DIFFRACTIONr_lrange_it8.0550.0736111
X-RAY DIFFRACTIONr_lrange_other8.05449.966080
X-RAY DIFFRACTIONr_ncsr_local_group_10.0970.0510497
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.097430.05008
12BX-RAY DIFFRACTIONLocal ncs0.097430.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.796-1.8430.3741470.3832702X-RAY DIFFRACTION67.3682
1.843-1.8930.3241570.3433246X-RAY DIFFRACTION82.1187
1.893-1.9480.3211830.3153148X-RAY DIFFRACTION83.5675
1.948-2.0080.3251640.2743050X-RAY DIFFRACTION83.9165
2.008-2.0730.2521420.2383112X-RAY DIFFRACTION86.153
2.073-2.1460.2151520.2092982X-RAY DIFFRACTION86.6464
2.146-2.2270.2251410.1882954X-RAY DIFFRACTION87.9012
2.227-2.3180.2091460.1752871X-RAY DIFFRACTION89.0759
2.318-2.4210.1931310.1562797X-RAY DIFFRACTION90.2033
2.421-2.5390.2061390.1492710X-RAY DIFFRACTION92.0517
2.539-2.6760.231280.1682617X-RAY DIFFRACTION93.1772
2.676-2.8380.2081320.1552486X-RAY DIFFRACTION94.7864
2.838-3.0330.1951340.1582433X-RAY DIFFRACTION96.2505
3.033-3.2750.2031170.1782235X-RAY DIFFRACTION98.2456
3.275-3.5870.173880.1672159X-RAY DIFFRACTION99.778
3.587-4.0080.185920.1521932X-RAY DIFFRACTION100
4.008-4.6240.142960.1281704X-RAY DIFFRACTION100
4.624-5.6540.158750.1481441X-RAY DIFFRACTION100
5.654-7.9570.194510.1721114X-RAY DIFFRACTION100

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