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- PDB-9e0c: Structure of proline utilization A complexed with 1-benzofuran-5-... -

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Basic information

Entry
Database: PDB / ID: 9e0c
TitleStructure of proline utilization A complexed with 1-benzofuran-5-ylmethanol
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 / 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: 1.32 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)268,94228
Polymers263,9232
Non-polymers5,01826
Water46,4252577
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12480 Å2
ΔGint-145 kcal/mol
Surface area76930 Å2
MethodPISA
2
A: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,32213
Polymers131,9621
Non-polymers2,36012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,62015
Polymers131,9621
Non-polymers2,65814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.369, 101.642, 125.924
Angle α, β, γ (deg.)90.00, 106.42, 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, 2603 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.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-A1BDX / (1-benzofuran-5-yl)methanol


Mass: 148.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8O2 / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: Chemical
ChemComp-SO4 / SULFATE ION


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


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


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#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.: 2577 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
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-benzofuran-5- ...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-benzofuran-5-ylmethanol. Crystal was soaked in cryobuffer containing 50 mM 1-benzofuran-5-ylmethanol 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: 1.00009 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: 1.00009 Å / Relative weight: 1
ReflectionResolution: 1.32→48.14 Å / Num. obs: 1044248 / % possible obs: 93.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.025 / Rrim(I) all: 0.065 / Χ2: 0.89 / Net I/σ(I): 14.1
Reflection shellResolution: 1.32→1.34 Å / % possible obs: 60.3 % / Redundancy: 4.8 % / Rmerge(I) obs: 1.757 / Num. measured all: 80388 / Num. unique obs: 16856 / CC1/2: 0.369 / Rpim(I) all: 0.884 / Rrim(I) all: 1.975 / Χ2: 0.58 / 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: 1.32→48.14 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 21.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1904 52912 5.07 %
Rwork0.1724 --
obs0.1733 1044248 93.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.32→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17809 0 326 2577 20712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618904
X-RAY DIFFRACTIONf_angle_d0.89925851
X-RAY DIFFRACTIONf_dihedral_angle_d16.4467093
X-RAY DIFFRACTIONf_chiral_restr0.0683035
X-RAY DIFFRACTIONf_plane_restr0.0083339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.340.326310700.325820391X-RAY DIFFRACTION57
1.34-1.350.342211360.320522220X-RAY DIFFRACTION63
1.35-1.370.33313530.315524217X-RAY DIFFRACTION68
1.37-1.380.323413860.305426472X-RAY DIFFRACTION75
1.38-1.40.308615440.291228612X-RAY DIFFRACTION81
1.4-1.420.301416960.283131405X-RAY DIFFRACTION88
1.42-1.440.288118690.266835150X-RAY DIFFRACTION99
1.44-1.460.269519290.257435233X-RAY DIFFRACTION100
1.46-1.490.269719290.246535413X-RAY DIFFRACTION100
1.49-1.510.255720160.233535178X-RAY DIFFRACTION100
1.51-1.540.24219230.2235377X-RAY DIFFRACTION100
1.54-1.570.229518610.213735386X-RAY DIFFRACTION100
1.57-1.60.220818570.206435404X-RAY DIFFRACTION99
1.6-1.630.225918570.203835064X-RAY DIFFRACTION99
1.63-1.660.221718280.202335239X-RAY DIFFRACTION99
1.66-1.70.230119150.195435116X-RAY DIFFRACTION99
1.7-1.740.217317380.192535022X-RAY DIFFRACTION98
1.74-1.790.217317530.187134788X-RAY DIFFRACTION98
1.79-1.840.202519010.180234290X-RAY DIFFRACTION96
1.84-1.90.209418760.184532541X-RAY DIFFRACTION92
1.9-1.970.207119030.183734674X-RAY DIFFRACTION98
1.97-2.050.199217580.169835477X-RAY DIFFRACTION100
2.05-2.140.186318820.166835263X-RAY DIFFRACTION99
2.14-2.260.183819160.16235251X-RAY DIFFRACTION99
2.26-2.40.185919260.161435155X-RAY DIFFRACTION99
2.4-2.580.180618600.163435193X-RAY DIFFRACTION99
2.58-2.840.178218720.163934897X-RAY DIFFRACTION98
2.84-3.250.178316860.16334251X-RAY DIFFRACTION96
3.26-4.10.156617040.140933252X-RAY DIFFRACTION94
4.1-48.140.14919680.140635405X-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)
10.599-0.0260.16210.1048-0.01490.1131-0.0312-0.10390.00580.03080.03790.0108-0.0178-0.0196-0.00640.14020.01890.0160.12490.00530.1231-25.706766.191592.6346
20.186-0.01520.08240.2108-0.04630.39250.016-0.0356-0.00790.04830.0061-0.00360.0443-0.0863-0.02380.1024-0.00230.00060.1109-0.01190.10745.645431.596791.1531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and peptide
2X-RAY DIFFRACTION2chain B and peptide

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