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- PDB-9dtl: Crystal Structure of C4-Dicarboxylate-Binding Protein (PA0884) of... -

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Basic information

Entry
Database: PDB / ID: 9dtl
TitleCrystal Structure of C4-Dicarboxylate-Binding Protein (PA0884) of Tripartite ATP-independent Periplasmic Transporter Family from Pseudomonas aeruginosa PAO1 in Complex with Succinic Acid
ComponentsC4-dicarboxylate-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID / Trap Periplasmic Solute Binding Protein / C4-dicarboxylate-binding protein / Succinic acid
Function / homology
Function and homology information


C4-dicarboxylate transport / transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function
TRAP transporter solute receptor, DctP family / 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
SUCCINIC ACID / Probable C4-dicarboxylate-binding periplasmic protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsMinasov, G. / Shukla, S. / Shuvalova, L. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal Structure of C4-Dicarboxylate-Binding Protein (PA0884) of Tripartite ATP-independent Periplasmic Transporter Family from Pseudomonas aeruginosa PAO1 in Complex with Succinic Acid
Authors: Minasov, G. / Shukla, S. / Shuvalova, L. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionOct 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C4-dicarboxylate-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7933
Polymers35,5831
Non-polymers2102
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.010, 67.095, 86.653
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein C4-dicarboxylate-binding periplasmic protein


Mass: 35582.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0884 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9I561
#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
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: 1.91 Å3/Da / Density % sol: 35.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: Protein: 8.4 mg/ml, 0.15M Sodium chloride, 0.02M Tris-HCl (pH 8.0), 2mM Succinic acid; Screen: Classics II (A4), 0.1M SPG buffer pH 7, 25% (w/v) PEG 1500; Cryo: Reservoir.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 8, 2022
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. obs: 65543 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 13.6 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.037 / Rrim(I) all: 0.099 / Rsym value: 0.092 / Χ2: 1.518 / Net I/σ(I): 25
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3205 / CC1/2: 0.661 / CC star: 0.892 / Rpim(I) all: 0.502 / Χ2: 1.004 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→28.55 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.875 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19533 3345 5.1 %RANDOM
Rwork0.17197 ---
obs0.17314 62134 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.357 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å2-0 Å20 Å2
2---0.88 Å20 Å2
3----0.42 Å2
Refinement stepCycle: 1 / Resolution: 1.3→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2329 0 14 335 2678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122550
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162456
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.8363452
X-RAY DIFFRACTIONr_angle_other_deg0.4471.7775635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6435318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.599524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.58710440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.023160
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02646
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_it0.8760.9861233
X-RAY DIFFRACTIONr_mcbond_other0.8750.9861233
X-RAY DIFFRACTIONr_mcangle_it1.3351.771555
X-RAY DIFFRACTIONr_mcangle_other1.3371.7711556
X-RAY DIFFRACTIONr_scbond_it1.9411.2781317
X-RAY DIFFRACTIONr_scbond_other1.9421.281318
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1072.231895
X-RAY DIFFRACTIONr_long_range_B_refined5.22314.782954
X-RAY DIFFRACTIONr_long_range_B_other5.06111.912846
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.301→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 228 -
Rwork0.274 4456 -
obs--96.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.59350.01331.07820.1893-0.00821.6506-0.067-0.17450.17470.09950.0269-0.0568-0.10650.01390.04010.071-0.0101-0.03230.0932-0.04530.083620.990529.761233.799
21.36230.26980.18080.75320.05640.66250.0153-0.0421-0.04860.08480.0304-0.12990.06740.0907-0.04560.01680.0119-0.0150.0458-0.01240.03617.058314.153624.6282
30.7431-0.02020.21650.57640.14940.73170.02650.0199-0.00610.0091-0.0024-0.03670.01670.0095-0.02410.01440.0028-0.00290.044-0.0050.01819.923620.081917.8229
40.8207-0.3278-0.0471.6286-0.01490.8217-0.0357-0.0065-0.0941-0.02670.01120.1159-0.016-0.09790.02460.00360.00330.0060.0726-0.00430.0585-2.454317.920316.7413
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 63
2X-RAY DIFFRACTION2A64 - 139
3X-RAY DIFFRACTION3A140 - 269
4X-RAY DIFFRACTION4A270 - 313

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