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

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Basic information

Entry
Database: PDB / ID: 9dwo
TitleCrystal Structure of C4-Dicarboxylate-Binding Protein (PA0884) of Tripartite ATP-independent Periplasmic Transporter Family from Pseudomonas aeruginosa PAO1 in Complex with L-Malate
ComponentsC4-dicarboxylate-binding protein
KeywordsTRANSPORT PROTEIN / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID / Trap Periplasmic Solute Binding Protein / C4-dicarboxylate-binding protein / L-Malate
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
(2S)-2-hydroxybutanedioic acid / Probable C4-dicarboxylate-binding periplasmic protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 L-Malate
Authors: Minasov, G. / Shukla, S. / Shuvalova, L. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionOct 9, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,3422
Polymers35,2081
Non-polymers1341
Water6,377354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.678, 66.953, 87.688
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 protein / DctP


Mass: 35207.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA0884 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I561
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 9
Details: Protein: 8.5 mg/ml, 0.15M Sodium chloride, 0.02M Tris-HCl (pH 8.0), 2mM L-Malate; Screen: PACT (D6), 0.1M MMT buffer pH 9.0, 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-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: 1.5→30 Å / Num. obs: 44360 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 12.5 % / Biso Wilson estimate: 12.8 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.04 / Rrim(I) all: 0.146 / Rsym value: 0.14 / Χ2: 1.042 / Net I/σ(I): 18.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2172 / CC1/2: 0.607 / CC star: 0.869 / Rpim(I) all: 0.356 / Χ2: 1.006 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→28.84 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.265 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21209 2200 5 %RANDOM
Rwork0.17463 ---
obs0.17648 41929 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.349 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å2-0 Å2
2---1.12 Å2-0 Å2
3---0.94 Å2
Refinement stepCycle: 1 / Resolution: 1.5→28.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 9 354 2683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122500
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162400
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.8393391
X-RAY DIFFRACTIONr_angle_other_deg0.4781.785510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6675314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.887523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.93810455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.020.023111
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02635
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_it1.0470.7561214
X-RAY DIFFRACTIONr_mcbond_other1.0470.7551214
X-RAY DIFFRACTIONr_mcangle_it1.571.3541536
X-RAY DIFFRACTIONr_mcangle_other1.5761.3561537
X-RAY DIFFRACTIONr_scbond_it2.3561.0571286
X-RAY DIFFRACTIONr_scbond_other2.3571.0581285
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7021.8031854
X-RAY DIFFRACTIONr_long_range_B_refined6.05414.023077
X-RAY DIFFRACTIONr_long_range_B_other5.84610.712933
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 160 -
Rwork0.269 3073 -
obs--98.78 %
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)
12.2036-0.32871.13511.03920.67842.6615-0.1387-0.32760.30040.23480.1478-0.0829-0.22840.1743-0.00920.1667-0.0309-0.02030.1314-0.07620.087120.422129.481234.1949
21.49550.40630.3051.02950.31041.05560.0687-0.1034-0.05180.1570.0023-0.1410.09950.1292-0.0710.04310.0011-0.0160.0432-0.00820.023317.19414.141325.1568
31.1461-0.2560.11781.17850.2391.36170.05850.04150.0207-0.0185-0.0144-0.0558-0.01630.0327-0.04420.0384-0.00190.01570.0292-0.00080.009110.166219.985818.0617
41.1083-0.3896-0.09232.330.27331.11730.00870.0357-0.1330.0043-0.06160.1703-0.0148-0.1970.05290.01710.00880.00630.0437-0.01060.0271-2.285717.914616.5735
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 62
2X-RAY DIFFRACTION2A63 - 139
3X-RAY DIFFRACTION3A140 - 269
4X-RAY DIFFRACTION4A270 - 313

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