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

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Basic information

Entry
Database: PDB / ID: 9dwp
TitleCrystal Structure of C4-Dicarboxylate-Binding Protein (PA0884) of Tripartite ATP-independent Periplasmic Transporter Family from Pseudomonas aeruginosa PAO1 in Complex with Mesaconic Acid
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 / Mesaconic 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
(2E)-2-METHYLBUT-2-ENEDIOIC ACID / Probable C4-dicarboxylate-binding periplasmic protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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 Mesaconic Acid
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,4225
Polymers35,2081
Non-polymers2144
Water8,125451
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.520, 67.200, 60.469
Angle α, β, γ (deg.)90.00, 106.47, 90.00
Int Tables number4
Space group name H-MP1211

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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-MEZ / (2E)-2-METHYLBUT-2-ENEDIOIC ACID / MESACONIC ACID / MESACONATE


Mass: 130.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 1.93 Å3/Da / Density % sol: 36.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 8.5 mg/ml, 0.15M Sodium chloride, 0.02M Tris-HCl (pH 8.0), 2mM Mesaconic Acid; Screen: PEGs II (D11), 0.2M Magnesium chloride, 0.1M Tris (pH 8.5), 30% (w/v) PEG 4000; 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: 1.32→30 Å / Num. obs: 61217 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 9.1 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.051 / Rrim(I) all: 0.103 / Rsym value: 0.089 / Χ2: 1.003 / Net I/σ(I): 14.5
Reflection shellResolution: 1.32→1.34 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.771 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3117 / CC1/2: 0.575 / CC star: 0.854 / Rpim(I) all: 0.445 / Rrim(I) all: 0.895 / Rsym value: 0.771 / Χ2: 1.001 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→29.7 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.75 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17727 3012 4.9 %RANDOM
Rwork0.15757 ---
obs0.15853 58148 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.894 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å2-0.04 Å2
2--0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.32→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 12 451 2914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0122698
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162577
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.8353668
X-RAY DIFFRACTIONr_angle_other_deg0.4851.7785910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.265343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.518524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.11610483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.023405
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02683
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_it0.8490.6431327
X-RAY DIFFRACTIONr_mcbond_other0.8240.6421327
X-RAY DIFFRACTIONr_mcangle_it1.3421.151685
X-RAY DIFFRACTIONr_mcangle_other1.3441.1531686
X-RAY DIFFRACTIONr_scbond_it1.6890.881371
X-RAY DIFFRACTIONr_scbond_other1.690.8811370
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7311.5131983
X-RAY DIFFRACTIONr_long_range_B_refined4.9512.493326
X-RAY DIFFRACTIONr_long_range_B_other4.6959.063155
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.32→1.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 224 -
Rwork0.269 4226 -
obs--97.91 %
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)
10.73970.2641-0.28320.4166-0.20582.38770.0404-0.06530.0430.0389-0.01580.017-0.0623-0.0861-0.02460.02130.00380.010.0207-0.00460.00720.129513.599935.7873
20.4320.13630.08510.48270.06820.53310.00230.0097-0.0244-0.00580.0242-0.02340.01170.0433-0.02650.00410.00550.00360.02120.0020.0078.01092.548123.0009
30.27810.0296-0.0970.2012-0.11160.929-0.01070.01420.0123-0.01650.0140.0062-0.00460.0143-0.00330.0059-0.00240.00030.01380.00220.00124.907110.332214.9763
40.9566-0.6221-0.03870.66390.04380.8950.02550.0607-0.0553-0.0634-0.00790.08540.0275-0.0717-0.01760.0143-0.0117-0.01460.02460.01610.0273-2.39417.65765.0692
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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