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- PDB-9dl3: Structure of proline utilization A complexed with quinoline-2-car... -

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Basic information

Entry
Database: PDB / ID: 9dl3
TitleStructure of proline utilization A complexed with quinoline-2-carboxylic acid
ComponentsBifunctional protein PutA
KeywordsOXIDOREDUCTASE / FLAVOENZYME / ROSSMANN FOLD / PROLINE DEHYDROGENASE / ALDEHYDE DEHYDROGENASE / PROLINE CATABOLISM / SUBSTRATE CHANNELING / BIFUNCTIONAL ENZYME
Function / homology
Function and homology information


proline dehydrogenase / proline dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / L-glutamate gamma-semialdehyde dehydrogenase activity / L-proline catabolic process to L-glutamate / proline biosynthetic process / cytoplasmic side of plasma membrane / DNA-binding transcription factor activity / nucleotide binding / DNA binding
Similarity search - Function
Proline dehydrogenase PutA, domain I / Proline utilization A proline dehydrogenase N-terminal domain / Proline utilization A proline dehydrogenase N-terminal domain / Delta-1-pyrroline-5-carboxylate dehydrogenase 3 / Proline dehydrogenase PutA, domain II / Proline dehydrogenase PutA, domain I/II / DNA-binding domain of Proline dehydrogenase / Bifunctional protein PutA / Proline dehydrogenase domain / Proline dehydrogenase ...Proline dehydrogenase PutA, domain I / Proline utilization A proline dehydrogenase N-terminal domain / Proline utilization A proline dehydrogenase N-terminal domain / Delta-1-pyrroline-5-carboxylate dehydrogenase 3 / Proline dehydrogenase PutA, domain II / Proline dehydrogenase PutA, domain I/II / DNA-binding domain of Proline dehydrogenase / Bifunctional protein PutA / Proline dehydrogenase domain / Proline dehydrogenase / : / FAD-linked oxidoreductase-like / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FORMIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / quinoline-2-carboxylic acid / Bifunctional protein PutA
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.77 Å
AuthorsTanner, J.J. / Meeks, K.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132640 United States
CitationJournal: Molecules / Year: 2024
Title: Crystallographic Fragment Screening of a Bifunctional Proline Catabolic Enzyme Reveals New Inhibitor Templates for Proline Dehydrogenase and L-Glutamate-gamma-semialdehyde Dehydrogenase.
Authors: Meeks, K.R. / Bogner, A.N. / Nix, J.C. / Tanner, J.J.
History
DepositionSep 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional protein PutA
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,65542
Polymers263,9232
Non-polymers5,73140
Water39,8852214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14890 Å2
ΔGint-138 kcal/mol
Surface area79750 Å2
MethodPISA
2
A: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,82221
Polymers131,9621
Non-polymers2,86020
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,83321
Polymers131,9621
Non-polymers2,87220
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.961, 102.330, 127.061
Angle α, β, γ (deg.)90.00, 105.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bifunctional protein PutA


Mass: 131961.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: SM11 / Gene: putA, SM11_chr0102 / Production host: Escherichia coli (E. coli)
References: UniProt: F7X6I3, proline dehydrogenase, L-glutamate gamma-semialdehyde dehydrogenase

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Non-polymers , 9 types, 2254 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-QNC / quinoline-2-carboxylic acid


Mass: 173.168 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2214 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir contained 0.1 M HEPES, pH 7.5, 0.1 M sodium formate, 0.1 M magnesium chloride, 0.15 M ammonium sulfate, and 22% (w/v) PEG 3350. Crystal was soaked in cryobuffer containing 50 mM ...Details: Reservoir contained 0.1 M HEPES, pH 7.5, 0.1 M sodium formate, 0.1 M magnesium chloride, 0.15 M ammonium sulfate, and 22% (w/v) PEG 3350. Crystal was soaked in cryobuffer containing 50 mM quinoline-2-carboxylic acid and 20% PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.072156 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jun 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072156 Å / Relative weight: 1
ReflectionResolution: 1.77→48.53 Å / Num. obs: 412629 / % possible obs: 95.5 % / Redundancy: 3.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.051 / Rrim(I) all: 0.094 / Χ2: 1 / Net I/σ(I): 12.3
Reflection shellResolution: 1.77→1.8 Å / % possible obs: 73.2 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.917 / Num. measured all: 20177 / Num. unique obs: 8678 / CC1/2: 0.426 / Rpim(I) all: 0.749 / Rrim(I) all: 1.192 / Χ2: 0.55 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.77→48.53 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2129 8529 2.07 %
Rwork0.1767 --
obs0.1774 412629 86.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17608 0 372 2214 20194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618595
X-RAY DIFFRACTIONf_angle_d0.84425351
X-RAY DIFFRACTIONf_dihedral_angle_d14.5276844
X-RAY DIFFRACTIONf_chiral_restr0.0482954
X-RAY DIFFRACTIONf_plane_restr0.0083280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.790.34941730.3029058X-RAY DIFFRACTION58
1.79-1.810.3642110.29439716X-RAY DIFFRACTION63
1.81-1.830.33412370.290210462X-RAY DIFFRACTION67
1.83-1.860.31582450.279511069X-RAY DIFFRACTION71
1.86-1.880.29412610.28411490X-RAY DIFFRACTION75
1.88-1.910.34092660.321411924X-RAY DIFFRACTION76
1.91-1.930.3352810.296813035X-RAY DIFFRACTION84
1.93-1.960.26682770.252214641X-RAY DIFFRACTION94
1.96-1.990.28223190.239615027X-RAY DIFFRACTION97
1.99-2.030.23383360.223114890X-RAY DIFFRACTION96
2.03-2.060.33120.234613973X-RAY DIFFRACTION90
2.06-2.10.27622910.215314257X-RAY DIFFRACTION92
2.1-2.140.24112770.202514261X-RAY DIFFRACTION91
2.14-2.180.25452960.198913711X-RAY DIFFRACTION88
2.18-2.230.25672760.205412870X-RAY DIFFRACTION83
2.23-2.280.2692510.217712082X-RAY DIFFRACTION78
2.28-2.340.222850.184313617X-RAY DIFFRACTION88
2.34-2.40.21143090.173513836X-RAY DIFFRACTION89
2.4-2.470.20992800.177914150X-RAY DIFFRACTION91
2.47-2.550.21382940.172814694X-RAY DIFFRACTION94
2.55-2.640.22022880.167814914X-RAY DIFFRACTION96
2.64-2.750.24163010.168714543X-RAY DIFFRACTION93
2.75-2.870.23963470.168114736X-RAY DIFFRACTION95
2.87-3.030.17112970.163414559X-RAY DIFFRACTION94
3.03-3.220.19733530.163214322X-RAY DIFFRACTION93
3.22-3.460.19262900.156814104X-RAY DIFFRACTION90
3.46-3.810.1612890.139113940X-RAY DIFFRACTION90
3.81-4.360.15092820.125814217X-RAY DIFFRACTION91
4.36-5.50.16443020.132214900X-RAY DIFFRACTION96
5.5-48.530.16423030.152315102X-RAY DIFFRACTION97
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)
10.424-0.03790.22910.1224-0.00280.35710.01380.03540.02740.02520.0116-0.02050.01520.0197-0.02640.139-0.00510.01530.10340.01120.1342-25.886466.794894.7756
20.1653-0.0295-0.01110.2587-0.10830.23850.00510.01960.00340.0280.0018-0.0090.0009-0.0213-0.00930.1176-0.00350.00960.1518-0.01320.13136.813631.831191.4527
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and peptide
2X-RAY DIFFRACTION2chain B and peptide

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