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

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Entry
Database: PDB / ID: 9dsy
TitleCrystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite ATP-independent Periplasmic Transporter Family from Pseudomonas aeruginosa PAO1 in Complex with Succinic Acid
ComponentsC4-dicarboxylate-binding periplasmic protein DctP
KeywordsTRANSPORT PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / DctP / Succinic acid / 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 / SUCCINIC ACID / C4-dicarboxylate-binding periplasmic protein DctP
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 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 Succinic Acid
Authors: Minasov, G. / Shukla, S. / Shuvalova, L. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionSep 30, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,8687
Polymers35,4231
Non-polymers4456
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, 4O94
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.585, 44.495, 47.239
Angle α, β, γ (deg.)78.78, 84.22, 75.83
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 PAO1 (bacteria) / Strain: PAO1 / Gene: dctP, PA5167 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9HU18
#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-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.: 261 / 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: 1.97 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: Protein: 7.0 mg/ml, 0.5M Sodium chloride, 0.02M Tris-HCl (pH 8.0), 2mM Succinic acid; Screen: Classics II (H9), 0.05M Zing acetate, 20% (w/v) PEG 3350; 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: 1.35→30 Å / Num. obs: 55717 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 13.7 Å2 / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.063 / Rrim(I) all: 0.121 / Rsym value: 0.103 / Χ2: 1.01 / Net I/σ(I): 13.4
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 2681 / CC1/2: 0.559 / CC star: 0.847 / Rpim(I) all: 0.894 / Χ2: 0.994 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.35→29.85 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.409 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18922 2775 5 %RANDOM
Rwork0.17282 ---
obs0.17365 52942 95.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.752 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20.02 Å2
2---0.73 Å20.12 Å2
3---0.66 Å2
Refinement stepCycle: 1 / Resolution: 1.35→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 13 261 2685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122687
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162606
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.8393643
X-RAY DIFFRACTIONr_angle_other_deg0.4971.7776036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.315343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.436512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.35610475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.023226
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02604
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_it1.0221.0631327
X-RAY DIFFRACTIONr_mcbond_other1.0211.0621327
X-RAY DIFFRACTIONr_mcangle_it1.581.9061685
X-RAY DIFFRACTIONr_mcangle_other1.5791.9071686
X-RAY DIFFRACTIONr_scbond_it2.2241.3531360
X-RAY DIFFRACTIONr_scbond_other2.2241.3541359
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4842.3581959
X-RAY DIFFRACTIONr_long_range_B_refined5.59515.43099
X-RAY DIFFRACTIONr_long_range_B_other5.5213.023021
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.352→1.387 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 184 -
Rwork0.264 3765 -
obs--90.57 %
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)
11.64620.2327-0.30832.3024-0.59430.6945-0.0593-0.0718-0.11510.0884-0.0016-0.16680.02060.01910.06090.02250.00230.00490.00340.00450.0418-6.13-28.3827-9.5474
20.1535-0.62110.04488.5495-2.62514.0809-0.06640.1621-0.0765-0.42420.25180.30150.2566-0.5033-0.18530.1751-0.1392-0.0010.3287-0.08310.0594-15.4416-29.8115-30.0904
31.7517-1.28250.28383.2867-1.15760.98540.00650.31760.0474-0.5631-0.0557-0.18050.208-0.06640.04920.1353-0.03850.0310.07610.00270.0508-10.8414-22.462-24.6788
41.5236-0.4263-0.44131.7959-0.42682.87220.05630.30260.3267-0.216-0.1237-0.2231-0.09020.05430.06740.0662-0.01150.02510.08040.07240.0901-6.5527-9.6796-26.1241
51.1109-0.19690.09341.8745-0.34330.3279-0.04020.05-0.0201-0.09230.03940.03950.02410.00410.00080.0173-0.00790.00340.0052-00.0346-13.9686-23.5004-15.2785
63.7081-0.8833-1.75382.15450.58461.94850.04150.8360.1186-0.4921-0.18550.3504-0.0612-0.31540.1440.1346-0.002-0.09530.19850.04270.1034-19.9946-13.1725-31.0825
713.22735.5852-1.46733.7704-1.58332.2670.37890.4214-0.3681-0.4495-0.2232-0.06140.4775-0.0149-0.15560.3750.0451-0.01130.3267-0.08180.0542-8.1305-30.359-37.5487
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 105
2X-RAY DIFFRACTION2A106 - 125
3X-RAY DIFFRACTION3A126 - 162
4X-RAY DIFFRACTION4A163 - 197
5X-RAY DIFFRACTION5A198 - 280
6X-RAY DIFFRACTION6A281 - 312
7X-RAY DIFFRACTION7A313 - 328

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