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- PDB-9dy3: Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein... -

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Basic information

Entry
Database: PDB / ID: 9dy3
TitleCrystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite ATP-independent Periplasmic Transporter Family from Pseudomonas aeruginosa PAO1 in Complex with L-Malate
ComponentsC4-dicarboxylate-binding periplasmic protein DctP
KeywordsTRANSPORT PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / DctP / L-Malate / Center for Structural Biology of Infectious Diseases / CSBID
Function / homologyC4-dicarboxylate transport / TRAP transporter solute receptor, DctP family / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / transmembrane transport / outer membrane-bounded periplasmic space / (2S)-2-hydroxybutanedioic acid / C4-dicarboxylate-binding periplasmic protein DctP
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 Periplasmic Protein (PA5167) of Tripartite ATP-independent Periplasmic Transporter Family from Pseudomonas aeruginosa PAO1 in Complex with L-Malate.
Authors: Minasov, G. / Shukla, S. / Shuvalova, L. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionOct 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: 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 DctP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8847
Polymers35,4231
Non-polymers4616
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-149 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.505, 44.532, 46.886
Angle α, β, γ (deg.)78.95, 84.44, 75.84
Int Tables number1
Space group name H-MP1

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Components

#1: Protein C4-dicarboxylate-binding periplasmic protein DctP


Mass: 35423.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: dctP, PA5167 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HU18
#2: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 1.96 Å3/Da / Density % sol: 37.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein: 7.0 mg/ml, 0.5M Sodium chloride, 0.02M Tris-HCl (pH 8.0), 2mM L-Malate; Screen: PACT (B8), 0.2 M Ammonium chloride, 0.1 M MES (pH 6.0), 20% (w/v) PEG 6000; Cryo: Reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12723 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 19, 2022
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12723 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. obs: 56875 / % possible obs: 87.3 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 11.6 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.028 / Rsym value: 0.047 / Χ2: 1.013 / Net I/σ(I): 25.2
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 2346 / CC1/2: 0.898 / CC star: 0.973 / Rpim(I) all: 0.221 / Rrim(I) all: 0.432 / Rsym value: 0.371 / Χ2: 0.998 / % possible all: 71.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→29.84 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.741 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16739 2880 5.1 %RANDOM
Rwork0.14026 ---
obs0.14167 53993 87.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0.15 Å2-0.03 Å2
2---0.96 Å20.31 Å2
3---1.4 Å2
Refinement stepCycle: 1 / Resolution: 1.3→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 14 270 2704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122727
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162621
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.8413698
X-RAY DIFFRACTIONr_angle_other_deg0.4741.7816074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5245349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.573512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.27610481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023300
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02622
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_it4.0571.7781345
X-RAY DIFFRACTIONr_mcbond_other4.0481.7771345
X-RAY DIFFRACTIONr_mcangle_it5.9053.1941711
X-RAY DIFFRACTIONr_mcangle_other5.9073.1961712
X-RAY DIFFRACTIONr_scbond_it4.9382.0681382
X-RAY DIFFRACTIONr_scbond_other4.9392.0691381
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4553.6831988
X-RAY DIFFRACTIONr_long_range_B_refined12.96522.133214
X-RAY DIFFRACTIONr_long_range_B_other11.94220.933132
X-RAY DIFFRACTIONr_rigid_bond_restr2.00735348
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 183 -
Rwork0.178 3440 -
obs--75.03 %

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