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- PDB-9dl5: Structure of proline utilization A complexed with 5-chloro-1-indanone -

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Basic information

Entry
Database: PDB / ID: 9dl5
TitleStructure of proline utilization A complexed with 5-chloro-1-indanone
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 / : / 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 / 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)269,45043
Polymers263,9232
Non-polymers5,52741
Water31,9231772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14910 Å2
ΔGint-283 kcal/mol
Surface area77880 Å2
MethodPISA
2
A: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,68320
Polymers131,9621
Non-polymers2,72219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,76723
Polymers131,9621
Non-polymers2,80522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.538, 101.077, 125.757
Angle α, β, γ (deg.)90.00, 106.31, 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 , 8 types, 1813 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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-A1BDA / 5-chloro-2,3-dihydro-1H-inden-1-one / 5-chloro-1-indanone


Mass: 166.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7ClO / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1772 / 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: 47.07 %
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, 0.1 M ammonium sulfate, and 16% (w/v) PEG 3350. Crystal was soaked in cryobuffer containing 10 mM 5- ...Details: Reservoir contained 0.1 M HEPES, pH 7.5, 0.1 M sodium formate, 0.1 M magnesium chloride, 0.1 M ammonium sulfate, and 16% (w/v) PEG 3350. Crystal was soaked in cryobuffer containing 10 mM 5-Chloro-1-indanone (10% DMSO) 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: 1.000024 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000024 Å / Relative weight: 1
ReflectionResolution: 1.77→48.25 Å / Num. obs: 436068 / % possible obs: 99.3 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.037 / Rrim(I) all: 0.069 / Χ2: 1.04 / Net I/σ(I): 15.2
Reflection shellResolution: 1.77→1.8 Å / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.834 / Num. measured all: 41392 / Num. unique obs: 11546 / CC1/2: 0.577 / Rpim(I) all: 0.511 / Rrim(I) all: 0.98 / Χ2: 0.96 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.77→46.62 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 21.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2061 21720 4.98 %
Rwork0.1731 --
obs0.1747 436068 94.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17427 0 342 1772 19541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618156
X-RAY DIFFRACTIONf_angle_d0.82124763
X-RAY DIFFRACTIONf_dihedral_angle_d13.5276526
X-RAY DIFFRACTIONf_chiral_restr0.0472909
X-RAY DIFFRACTIONf_plane_restr0.0083216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.790.35366920.304613821X-RAY DIFFRACTION94
1.79-1.810.31487040.284513811X-RAY DIFFRACTION94
1.81-1.830.28017650.267613881X-RAY DIFFRACTION94
1.83-1.860.27138120.261213719X-RAY DIFFRACTION94
1.86-1.880.28997210.249513751X-RAY DIFFRACTION94
1.88-1.910.29317270.241813957X-RAY DIFFRACTION94
1.91-1.930.26917630.231713804X-RAY DIFFRACTION95
1.93-1.960.26747100.225413866X-RAY DIFFRACTION94
1.96-1.990.25488000.216213666X-RAY DIFFRACTION94
1.99-2.030.26177300.213913865X-RAY DIFFRACTION94
2.03-2.060.21977000.200913896X-RAY DIFFRACTION94
2.06-2.10.23287160.186313914X-RAY DIFFRACTION95
2.1-2.140.23727100.185913867X-RAY DIFFRACTION95
2.14-2.180.22056830.176613974X-RAY DIFFRACTION95
2.18-2.230.20486820.176613747X-RAY DIFFRACTION94
2.23-2.280.21286550.169413483X-RAY DIFFRACTION91
2.28-2.340.20756680.1713224X-RAY DIFFRACTION90
2.34-2.40.22297550.169913886X-RAY DIFFRACTION95
2.4-2.470.21987330.168313912X-RAY DIFFRACTION95
2.47-2.550.217560.168613934X-RAY DIFFRACTION95
2.55-2.640.19886930.164914117X-RAY DIFFRACTION95
2.64-2.750.20927340.169913895X-RAY DIFFRACTION95
2.75-2.870.22597600.175413904X-RAY DIFFRACTION95
2.87-3.030.2087560.167813801X-RAY DIFFRACTION95
3.03-3.220.19437270.166513968X-RAY DIFFRACTION95
3.22-3.460.18137280.160913812X-RAY DIFFRACTION94
3.46-3.810.18416960.146513757X-RAY DIFFRACTION94
3.81-4.360.15366940.137913293X-RAY DIFFRACTION90
4.36-5.50.17447720.14713796X-RAY DIFFRACTION95
5.5-46.620.17336780.160214027X-RAY DIFFRACTION95
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)
10.4278-0.02510.14990.12020.04020.2574-0.0161-0.01230.00180.02380.02380.00430.00780.0164-0.00860.19950.00320.01650.15280.01370.1856-25.450166.62592.9808
20.2209-0.00990.12970.2512-0.08140.46210.0219-0.04380.00070.04770.0197-0.01520.0438-0.0904-0.04110.1228-0.0005-0.00080.1552-0.01260.14435.99431.762390.9365
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and peptide
2X-RAY DIFFRACTION2chain B and peptide

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