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- PDB-9dl4: Structure of proline utilization A complexed with 2-pyridinethiol -

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Basic information

Entry
Database: PDB / ID: 9dl4
TitleStructure of proline utilization A complexed with 2-pyridinethiol
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 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 2-PYRIDINETHIOL / Bifunctional protein PutA
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 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)267,58125
Polymers263,9232
Non-polymers3,65723
Water25,0951393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11070 Å2
ΔGint-83 kcal/mol
Surface area80200 Å2
MethodPISA
2
A: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,96914
Polymers131,9621
Non-polymers2,00813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,61111
Polymers131,9621
Non-polymers1,64910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.155, 102.373, 127.504
Angle α, β, γ (deg.)90.00, 106.29, 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, 1416 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PYS / 2-PYRIDINETHIOL


Mass: 111.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5NS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1393 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
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 25 mM 2- ...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 25 mM 2-pyridinethiol 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 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 Å / Relative weight: 1
ReflectionResolution: 1.8→48.55 Å / Num. obs: 426838 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.031 / Rrim(I) all: 0.081 / Χ2: 1.17 / Net I/σ(I): 14.8
Reflection shellResolution: 1.8→1.83 Å / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 1.19 / Num. measured all: 79769 / Num. unique obs: 11331 / CC1/2: 0.628 / Rpim(I) all: 0.483 / Rrim(I) all: 1.286 / Χ2: 0.93 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→40.77 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 25.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2242 20891 4.89 %
Rwork0.194 --
obs0.1955 426838 93.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→40.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17523 0 235 1393 19151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618176
X-RAY DIFFRACTIONf_angle_d0.82324778
X-RAY DIFFRACTIONf_dihedral_angle_d13.596568
X-RAY DIFFRACTIONf_chiral_restr0.0492913
X-RAY DIFFRACTIONf_plane_restr0.0083230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.34026820.284414361X-RAY DIFFRACTION100
1.82-1.840.31287220.285114524X-RAY DIFFRACTION100
1.84-1.860.35087600.303114246X-RAY DIFFRACTION100
1.86-1.890.42027740.353514237X-RAY DIFFRACTION99
1.89-1.910.72782710.68914669X-RAY DIFFRACTION33
1.91-1.940.55554760.5048377X-RAY DIFFRACTION58
1.94-1.970.31467460.275614429X-RAY DIFFRACTION100
1.97-20.27626960.250514377X-RAY DIFFRACTION100
2-2.030.26988610.232414397X-RAY DIFFRACTION100
2.03-2.060.27167840.220414366X-RAY DIFFRACTION100
2.06-2.10.25376890.209514446X-RAY DIFFRACTION100
2.1-2.130.24777200.198214445X-RAY DIFFRACTION100
2.13-2.180.25527130.209214405X-RAY DIFFRACTION100
2.18-2.220.34625890.307212558X-RAY DIFFRACTION87
2.22-2.270.57554130.49868070X-RAY DIFFRACTION56
2.27-2.320.27597180.230913663X-RAY DIFFRACTION95
2.32-2.380.23846770.185514450X-RAY DIFFRACTION100
2.38-2.440.22787260.187314532X-RAY DIFFRACTION100
2.44-2.510.22997950.187114288X-RAY DIFFRACTION100
2.51-2.60.21577330.189714489X-RAY DIFFRACTION100
2.6-2.690.23367770.18714300X-RAY DIFFRACTION100
2.69-2.80.23487420.189414369X-RAY DIFFRACTION100
2.8-2.920.2237030.187414467X-RAY DIFFRACTION100
2.92-3.080.21387610.19114322X-RAY DIFFRACTION99
3.08-3.270.21327620.187114332X-RAY DIFFRACTION99
3.27-3.520.19877160.173614259X-RAY DIFFRACTION99
3.52-3.880.18247400.165213659X-RAY DIFFRACTION95
3.88-4.440.16076760.138214198X-RAY DIFFRACTION98
4.44-5.590.16467580.144914344X-RAY DIFFRACTION100
5.59-40.770.15857110.152614368X-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)
10.9925-0.01290.28310.18610.02330.3104-0.0263-0.11270.03670.0650.04920.0223-0.0032-0.041-0.0240.22150.01190.0220.15220.0270.1588-25.783966.453693.8907
20.488-0.04160.24390.5247-0.13260.65010.0468-0.0264-0.08260.07540.0321-0.05010.116-0.0798-0.07880.1749-0.0072-0.01920.1839-0.03240.17336.051931.426191.9948
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and peptide
2X-RAY DIFFRACTION2chain B and peptide

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