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- PDB-7myb: Structure of proline utilization A with tetrahydrothiophene-2-car... -

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Basic information

Entry
Database: PDB / ID: 7myb
TitleStructure of proline utilization A with tetrahydrothiophene-2-carboxylate bound in the proline dehydrogenase active site
ComponentsBifunctional protein PutA
KeywordsOXIDOREDUCTASE / FLAVOENZYME / ROSSMANN FOLD / PROLINE DEHYDROGNEASE / ALDEHYDE DEHYDROGENASE / PROLINE CATABOLISM / SUBSTRATE CHANNELING / BIFUNCTIONAL ENZYME
Function / homology
Function and homology information


proline dehydrogenase / proline dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to 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, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / (2S)-thiolane-2-carboxylic acid / (2R)-thiolane-2-carboxylic acid / Bifunctional protein PutA
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.52 Å
AuthorsTanner, J.J. / Campbell, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM132640 United States
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Photoinduced Covalent Irreversible Inactivation of Proline Dehydrogenase by S-Heterocycles.
Authors: Campbell, A.C. / Prater, A.R. / Bogner, A.N. / Quinn, T.P. / Gates, K.S. / Becker, D.F. / Tanner, J.J.
History
DepositionMay 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)268,18919
Polymers263,9232
Non-polymers4,26617
Water43,9392439
1
A: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,13810
Polymers131,9621
Non-polymers2,1769
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,0529
Polymers131,9621
Non-polymers2,0908
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10730 Å2
ΔGint-107 kcal/mol
Surface area79390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.884, 103.024, 127.062
Angle α, β, γ (deg.)90.00, 106.44, 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 (strain SM11) (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, 2456 molecules

#2: Chemical ChemComp-UJM / (2S)-thiolane-2-carboxylic acid


Mass: 132.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UJP / (2R)-thiolane-2-carboxylic acid


Mass: 132.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: 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
#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.: 4 / 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2439 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein stock solution: 6 mg/mL PutA with 50 mM tetrahydrothiophene-2-carboxylate in a buffer containing 50 mM Tris (pH 8.0), 50 mM NaCl, 5% (w/v) glycerol, and 0.5 mM Tris(2-caboxyethyl) ...Details: Protein stock solution: 6 mg/mL PutA with 50 mM tetrahydrothiophene-2-carboxylate in a buffer containing 50 mM Tris (pH 8.0), 50 mM NaCl, 5% (w/v) glycerol, and 0.5 mM Tris(2-caboxyethyl)phosphine. Reservoir solution: 19 % PEG-3350, 0.2 M ammonium sulfate, 0.1 M magnesium chloride, 0.1 M HEPES (pH 8.0), and 0.1 M sodium formate. Cryo-buffer: reservoir supplemented with 15 % PEG-200. Crystals were grown and harvested in low-light conditions

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.518→103.02 Å / Num. obs: 383136 / % possible obs: 99.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 17.8
Reflection shellResolution: 1.52→1.54 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.492 / Num. unique obs: 18385 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5KF6

5kf6


Resolution: 1.52→97.72 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 17.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.186 19043 4.97 %
Rwork0.164 --
obs0.165 383088 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.82 Å2
Refinement stepCycle: LAST / Resolution: 1.52→97.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18030 0 275 2439 20744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.53570.25745470.22911577X-RAY DIFFRACTION94
1.5357-1.55380.25486170.216712189X-RAY DIFFRACTION100
1.5538-1.57280.24236020.210612251X-RAY DIFFRACTION100
1.5728-1.59270.2286680.19912100X-RAY DIFFRACTION100
1.5927-1.61360.22166290.196312147X-RAY DIFFRACTION99
1.6136-1.63570.22476320.191312107X-RAY DIFFRACTION99
1.6357-1.65910.2126260.185812113X-RAY DIFFRACTION99
1.6591-1.68390.22026600.183512012X-RAY DIFFRACTION99
1.6839-1.71020.20436080.179812181X-RAY DIFFRACTION100
1.7102-1.73820.19736530.17712190X-RAY DIFFRACTION100
1.7382-1.76820.21556660.179612166X-RAY DIFFRACTION100
1.7682-1.80040.20446540.175112149X-RAY DIFFRACTION99
1.8004-1.8350.20136550.174712150X-RAY DIFFRACTION100
1.835-1.87240.20146060.170812163X-RAY DIFFRACTION99
1.8724-1.91320.22246020.186612102X-RAY DIFFRACTION99
1.9132-1.95770.20716390.182312147X-RAY DIFFRACTION99
1.9577-2.00660.1916490.169211908X-RAY DIFFRACTION98
2.0066-2.06090.18586590.169112178X-RAY DIFFRACTION100
2.0609-2.12150.1976370.167912247X-RAY DIFFRACTION100
2.1215-2.190.19016480.164412162X-RAY DIFFRACTION99
2.19-2.26830.19526670.160712144X-RAY DIFFRACTION99
2.2683-2.35910.19375990.162612149X-RAY DIFFRACTION99
2.3591-2.46650.18136460.162312067X-RAY DIFFRACTION98
2.4665-2.59660.18145980.16211998X-RAY DIFFRACTION98
2.5966-2.75930.1916610.16412253X-RAY DIFFRACTION100
2.7593-2.97230.19865790.168412289X-RAY DIFFRACTION100
2.9723-3.27140.19296340.165412250X-RAY DIFFRACTION99
3.2714-3.74480.17166410.153912035X-RAY DIFFRACTION98
3.7448-4.71810.15386930.133212269X-RAY DIFFRACTION100
4.7181-97.7190.15056680.150512352X-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)
10.5344-0.02710.16720.1233-0.00020.1729-0.0086-0.0524-0.00950.01770.02930.0096-0.0079-0.0094-0.02050.15180.00820.01390.120.01070.1337-25.790466.20493.4756
20.19550.00090.03290.236-0.04940.2730.0051-0.0277-0.00240.04060.00210.00320.0106-0.0469-0.01090.09840.00460.00070.1007-0.01130.09215.669231.106292.1896
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A'
2X-RAY DIFFRACTION2CHAIN 'B'

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