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- PDB-9e0a: Structure of proline utilization A complexed with 1,4-benzenedime... -

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Basic information

Entry
Database: PDB / ID: 9e0a
TitleStructure of proline utilization A complexed with 1,4-benzenedimethanol
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: 1.39 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

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)268,14521
Polymers263,9232
Non-polymers4,22219
Water45,3982520
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11230 Å2
ΔGint-139 kcal/mol
Surface area77170 Å2
MethodPISA
2
A: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,17412
Polymers131,9621
Non-polymers2,21211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,9719
Polymers131,9621
Non-polymers2,0108
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.715, 102.066, 126.176
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 , 9 types, 2539 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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: 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
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-A1BDW / (1,4-phenylene)dimethanol


Mass: 138.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10O2 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2520 / 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: 2.36 Å3/Da / Density % sol: 47.83 %
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 1,4-benzenedimethanol. ...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 1,4-benzenedimethanol. Crystal was soaked in cryobuffer containing 50 mM 1,4-benzenedimethanol 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: 1.39→48.31 Å / Num. obs: 946557 / % possible obs: 98.3 % / Redundancy: 7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.03 / Rrim(I) all: 0.08 / Χ2: 0.96 / Net I/σ(I): 13.5
Reflection shellResolution: 1.39→1.41 Å / % possible obs: 95.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 2.493 / Num. measured all: 161024 / Num. unique obs: 23190 / CC1/2: 0.332 / Rpim(I) all: 1.009 / Rrim(I) all: 2.694 / Χ2: 0.66 / 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: 1.39→47.03 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1909 47595 5.03 %
Rwork0.1718 --
obs0.1728 946557 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.39→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17877 0 273 2520 20670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00518865
X-RAY DIFFRACTIONf_angle_d0.91225783
X-RAY DIFFRACTIONf_dihedral_angle_d16.5267084
X-RAY DIFFRACTIONf_chiral_restr0.0693021
X-RAY DIFFRACTIONf_plane_restr0.0083338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.410.339915290.33429082X-RAY DIFFRACTION95
1.41-1.420.33115290.318329641X-RAY DIFFRACTION96
1.42-1.440.315215400.31229916X-RAY DIFFRACTION97
1.44-1.460.305515230.301330050X-RAY DIFFRACTION98
1.46-1.480.32116380.295430164X-RAY DIFFRACTION98
1.48-1.50.31316240.289830040X-RAY DIFFRACTION98
1.5-1.520.297215650.271330187X-RAY DIFFRACTION98
1.52-1.540.263216850.254230073X-RAY DIFFRACTION98
1.54-1.570.268316930.2530086X-RAY DIFFRACTION98
1.57-1.590.258415510.232730387X-RAY DIFFRACTION99
1.59-1.620.248116630.225830113X-RAY DIFFRACTION98
1.62-1.650.236316760.215630145X-RAY DIFFRACTION98
1.65-1.680.233216060.211130180X-RAY DIFFRACTION98
1.68-1.710.236216440.213330270X-RAY DIFFRACTION99
1.71-1.750.21416680.202430259X-RAY DIFFRACTION99
1.75-1.790.226914950.19830109X-RAY DIFFRACTION98
1.79-1.840.206914700.186128715X-RAY DIFFRACTION93
1.84-1.890.219616010.185829230X-RAY DIFFRACTION95
1.89-1.940.20515070.185630345X-RAY DIFFRACTION98
1.94-20.196715370.179330410X-RAY DIFFRACTION99
2-2.080.19516400.169230167X-RAY DIFFRACTION98
2.08-2.160.194916610.164730274X-RAY DIFFRACTION99
2.16-2.260.180215690.162130196X-RAY DIFFRACTION98
2.26-2.380.194215150.164130373X-RAY DIFFRACTION98
2.38-2.530.176216820.159930094X-RAY DIFFRACTION98
2.53-2.720.176215470.159630208X-RAY DIFFRACTION98
2.72-2.990.191115580.162229770X-RAY DIFFRACTION97
2.99-3.430.174814500.157527536X-RAY DIFFRACTION90
3.43-4.320.14715730.13430310X-RAY DIFFRACTION99
4.32-47.030.1516560.137230632X-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)
10.6288-0.01430.16430.099-0.00050.1372-0.0351-0.1169-0.00510.03050.03320.0173-0.0114-0.01330.00220.16720.02050.01290.12910.00530.1354-25.652966.058692.7845
20.14680.00520.03460.2283-0.04750.28850.0038-0.03440.00020.04490.0018-0.00020.0168-0.065-0.00990.13220.0056-0.00070.1485-0.01910.13535.673731.357491.3171
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and peptide
2X-RAY DIFFRACTION2chain B and peptide

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