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- PDB-9e0e: Structure of proline utilization A complexed with (1H-indol-5-yl)... -

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Basic information

Entry
Database: PDB / ID: 9e0e
TitleStructure of proline utilization A complexed with (1H-indol-5-yl)methanol
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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Bifunctional protein PutA
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.37 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
DepositionOct 17, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)269,38232
Polymers263,9232
Non-polymers5,45930
Water39,8312211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14830 Å2
ΔGint-149 kcal/mol
Surface area76400 Å2
MethodPISA
2
A: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,42114
Polymers131,9621
Non-polymers2,45913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,96118
Polymers131,9621
Non-polymers3,00017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.457, 101.500, 125.333
Angle α, β, γ (deg.)90.00, 106.51, 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 , 10 types, 2241 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.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-A1BDU / (1H-indol-5-yl)methanol


Mass: 147.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9NO / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#8: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2211 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
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 18% (w/v) PEG 3350. Enzyme was incubated with 24 mM (1H-indol-5-yl) ...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 18% (w/v) PEG 3350. Enzyme was incubated with 24 mM (1H-indol-5-yl)methanol. The stock solution of (1H-indol-5-yl)methanol was resuspended in 50% (w/v) PEG 3350 for crystal studies. Crystal was soaked in cryobuffer containing 100 mM (1H-indol-5-yl)methanol and 20% PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00008 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00008 Å / Relative weight: 1
ReflectionResolution: 1.37→46.75 Å / Num. obs: 967998 / % possible obs: 97.8 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.031 / Rrim(I) all: 0.083 / Χ2: 0.9 / Net I/σ(I): 12.2
Reflection shellResolution: 1.37→1.39 Å / % possible obs: 91.1 % / Redundancy: 6.1 % / Rmerge(I) obs: 1.988 / Num. measured all: 137607 / Num. unique obs: 22701 / CC1/2: 0.285 / Rpim(I) all: 0.865 / Rrim(I) all: 2.175 / Χ2: 0.6 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.37→46.75 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 21.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.192 48800 5.04 %
Rwork0.173 --
obs0.174 967998 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.37→46.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17742 0 354 2211 20307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00518613
X-RAY DIFFRACTIONf_angle_d0.90225405
X-RAY DIFFRACTIONf_dihedral_angle_d16.0966870
X-RAY DIFFRACTIONf_chiral_restr0.0692985
X-RAY DIFFRACTIONf_plane_restr0.0073293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.336814810.335227987X-RAY DIFFRACTION89
1.39-1.40.32915870.323229529X-RAY DIFFRACTION94
1.4-1.420.321715720.314330321X-RAY DIFFRACTION95
1.42-1.440.327915640.302930612X-RAY DIFFRACTION97
1.44-1.460.305316330.290431070X-RAY DIFFRACTION98
1.46-1.480.295916270.274530823X-RAY DIFFRACTION98
1.48-1.50.279616680.258830908X-RAY DIFFRACTION98
1.5-1.520.251516730.24630990X-RAY DIFFRACTION98
1.52-1.540.258317000.234730796X-RAY DIFFRACTION98
1.54-1.570.252916940.226531061X-RAY DIFFRACTION98
1.57-1.60.230516570.21730897X-RAY DIFFRACTION98
1.6-1.620.224417290.211730865X-RAY DIFFRACTION98
1.62-1.660.223216800.203831035X-RAY DIFFRACTION98
1.66-1.690.22216750.199931081X-RAY DIFFRACTION98
1.69-1.730.22416920.19831098X-RAY DIFFRACTION99
1.73-1.770.217117210.1930977X-RAY DIFFRACTION98
1.77-1.810.200416110.184130602X-RAY DIFFRACTION97
1.81-1.860.200515340.178428940X-RAY DIFFRACTION92
1.86-1.910.209616530.183530848X-RAY DIFFRACTION98
1.91-1.980.203516280.177631191X-RAY DIFFRACTION99
1.98-2.050.194915790.169231178X-RAY DIFFRACTION98
2.05-2.130.190816310.165531177X-RAY DIFFRACTION98
2.13-2.230.173915650.160231064X-RAY DIFFRACTION98
2.23-2.340.183815380.163631085X-RAY DIFFRACTION98
2.34-2.490.189616380.163130859X-RAY DIFFRACTION98
2.49-2.680.184516890.164830757X-RAY DIFFRACTION97
2.68-2.950.186616050.164830470X-RAY DIFFRACTION96
2.95-3.380.173914730.162428703X-RAY DIFFRACTION91
3.38-4.260.15216080.138130827X-RAY DIFFRACTION97
4.26-46.750.162916950.145131447X-RAY DIFFRACTION100
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)
10.6044-0.0190.17570.0839-0.01270.1644-0.0426-0.08320.0120.02560.03550.0093-0.0165-0.01560.00630.15190.01870.01370.12340.00130.1364-25.777766.422392.204
20.188-0.00370.08870.1868-0.05990.43250.0161-0.0361-0.0060.03460.0007-0.00540.0406-0.0943-0.01950.1014-0.00190.00270.1224-0.01380.11735.674831.881390.5068
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and peptide
2X-RAY DIFFRACTION2chain B and peptide

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