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- PDB-9dl7: Structure of proline utilization A complexed with 1-(4-fluorophen... -

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Basic information

Entry
Database: PDB / ID: 9dl7
TitleStructure of proline utilization A complexed with 1-(4-fluorophenyl)thiourea
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
1-(4-fluorophenyl)thiourea / FLAVIN-ADENINE DINUCLEOTIDE / FORMIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Bifunctional protein PutA
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.72 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)270,03454
Polymers263,9232
Non-polymers6,11152
Water26,9861498
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16350 Å2
ΔGint-414 kcal/mol
Surface area79060 Å2
MethodPISA
2
A: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,35131
Polymers131,9621
Non-polymers3,39030
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,68323
Polymers131,9621
Non-polymers2,72122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.135, 101.867, 126.557
Angle α, β, γ (deg.)90.00, 106.38, 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 , 7 types, 1550 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-8P4 / 1-(4-fluorophenyl)thiourea


Mass: 170.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7FN2S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1498 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
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, 0.2 M ammonium sulfate, and 20% (w/v) PEG 3350. Crystal was soaked in cryobuffer containing 19 mM 1- ...Details: Reservoir contained 0.1 M HEPES, pH 7.5, 0.1 M sodium formate, 0.1 M magnesium chloride, 0.2 M ammonium sulfate, and 20% (w/v) PEG 3350. Crystal was soaked in cryobuffer containing 19 mM 1-(4-fluorophenyl)thiourea 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: 1.000018 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jul 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000018 Å / Relative weight: 1
ReflectionResolution: 1.72→46.97 Å / Num. obs: 503696 / % possible obs: 99.4 % / Redundancy: 6.5 % / CC1/2: 0.981 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.096 / Rrim(I) all: 0.238 / Χ2: 0.97 / Net I/σ(I): 6.2
Reflection shellResolution: 1.72→1.75 Å / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 2.356 / Num. measured all: 89890 / Num. unique obs: 12912 / CC1/2: 0.397 / Rpim(I) all: 0.953 / Rrim(I) all: 2.544 / Χ2: 0.4 / Net I/σ(I) obs: 0.6

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.72→46.97 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 10332 2.05 %
Rwork0.2084 --
obs0.2091 503696 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.72→46.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17530 0 370 1498 19398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618303
X-RAY DIFFRACTIONf_angle_d0.81324956
X-RAY DIFFRACTIONf_dihedral_angle_d13.3566570
X-RAY DIFFRACTIONf_chiral_restr0.0472919
X-RAY DIFFRACTIONf_plane_restr0.0073240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.740.31313340.302516724X-RAY DIFFRACTION99
1.74-1.760.37773530.29216784X-RAY DIFFRACTION100
1.76-1.780.30133370.28416746X-RAY DIFFRACTION100
1.78-1.80.32893920.278816812X-RAY DIFFRACTION100
1.8-1.830.28952930.286416741X-RAY DIFFRACTION100
1.83-1.850.30733590.292216794X-RAY DIFFRACTION100
1.85-1.880.34213720.332716601X-RAY DIFFRACTION99
1.88-1.910.44983100.416516356X-RAY DIFFRACTION97
1.91-1.940.43843800.437915893X-RAY DIFFRACTION95
1.94-1.970.4253580.359616616X-RAY DIFFRACTION99
1.97-20.31993150.271216772X-RAY DIFFRACTION100
2-2.040.27263220.25616740X-RAY DIFFRACTION99
2.04-2.080.33363260.291215538X-RAY DIFFRACTION92
2.08-2.120.26923890.233516606X-RAY DIFFRACTION99
2.12-2.170.21464020.204816732X-RAY DIFFRACTION100
2.17-2.220.26823450.21416672X-RAY DIFFRACTION100
2.22-2.270.3063580.245815858X-RAY DIFFRACTION95
2.27-2.330.21653850.206616618X-RAY DIFFRACTION99
2.33-2.40.22683540.19116712X-RAY DIFFRACTION99
2.4-2.480.20653240.187416786X-RAY DIFFRACTION99
2.48-2.570.24043130.193816655X-RAY DIFFRACTION99
2.57-2.670.22354090.199816459X-RAY DIFFRACTION98
2.67-2.790.24313300.198316469X-RAY DIFFRACTION98
2.79-2.940.23223100.193916554X-RAY DIFFRACTION98
2.94-3.130.23743160.19516404X-RAY DIFFRACTION97
3.13-3.370.22533640.19316128X-RAY DIFFRACTION96
3.37-3.710.21383300.184715346X-RAY DIFFRACTION92
3.71-4.240.20063090.165515584X-RAY DIFFRACTION92
4.24-5.340.18613060.161616102X-RAY DIFFRACTION95
5.34-46.970.17963370.163716562X-RAY DIFFRACTION99
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)
10.5087-0.0420.1440.14280.03470.2421-0.0089-0.02180.00660.030.0262-0.00290.00580.0134-0.01990.2407-0.00340.00530.19860.02270.196-25.723666.440893.4146
20.3158-0.01870.21860.2837-0.06840.63370.0419-0.0564-0.03620.06590.0343-0.01480.1084-0.1285-0.07050.16580.0002-0.01930.1973-0.01440.16365.956431.412291.4587
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and peptide
2X-RAY DIFFRACTION2chain B and peptide

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