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- PDB-8uq1: Minimal PutA proline dehydrogenase domain (design #2) complexed w... -

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Basic information

Entry
Database: PDB / ID: 8uq1
TitleMinimal PutA proline dehydrogenase domain (design #2) complexed with (Allylthio)acetic acid
ComponentsBifunctional protein PutA
KeywordsOXIDOREDUCTASE / BETA/ALPHA BARREL / FLAVOENZYME / PROLINE CATABOLISM
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 / DI(HYDROXYETHYL)ETHER / : / Bifunctional protein PutA
Similarity search - Component
Biological speciesSinorhizobium meliloti SM11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.41 Å
AuthorsTanner, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132640 United States
CitationJournal: Biochemistry / Year: 2024
Title: Noncovalent Inhibition and Covalent Inactivation of Proline Dehydrogenase by Analogs of N -Propargylglycine.
Authors: Tanner, J.J. / Ji, J. / Bogner, A.N. / Scott, G.K. / Patel, S.M. / Seravalli, J. / Gates, K.S. / Benz, C.C. / Becker, D.F.
History
DepositionOct 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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)89,5968
Polymers87,5482
Non-polymers2,0486
Water10,809600
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-33 kcal/mol
Surface area29550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.753, 54.938, 75.883
Angle α, β, γ (deg.)103.96, 100.43, 108.65
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Bifunctional protein PutA


Mass: 43773.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti SM11 (bacteria) / Gene: putA, SM11_chr0102, putA / Production host: Escherichia coli (E. coli)
References: UniProt: F7X6I3, proline dehydrogenase, L-glutamate gamma-semialdehyde dehydrogenase
#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.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-X7Q / (Allylthio)acetic acid


Mass: 132.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / Source method: isolated from a natural source / Formula: H2O
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: 2.05 Å3/Da / Density % sol: 39.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05 - 0.2 M sodium formate, 19 - 24% PEG 3350 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.41→49.3 Å / Num. obs: 115648 / % possible obs: 86.3 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.028 / Rrim(I) all: 0.054 / Net I/σ(I): 14.2 / Num. measured all: 428613
Reflection shellResolution: 1.41→1.43 Å / % possible obs: 80.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.443 / Num. measured all: 19599 / Num. unique obs: 5373 / CC1/2: 0.871 / Rpim(I) all: 0.27 / Rrim(I) all: 0.52 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.41→49.3 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 21.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2035 5639 4.89 %
Rwork0.1796 --
obs0.1807 115368 86.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.41→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5947 0 136 600 6683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056241
X-RAY DIFFRACTIONf_angle_d0.8658474
X-RAY DIFFRACTIONf_dihedral_angle_d12.1142248
X-RAY DIFFRACTIONf_chiral_restr0.07953
X-RAY DIFFRACTIONf_plane_restr0.0081079
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.430.29291940.25273362X-RAY DIFFRACTION80
1.43-1.440.23631710.24533479X-RAY DIFFRACTION80
1.44-1.460.27651630.23033175X-RAY DIFFRACTION76
1.46-1.480.24521770.21753720X-RAY DIFFRACTION86
1.48-1.50.25131610.20323614X-RAY DIFFRACTION86
1.5-1.520.20631930.20533710X-RAY DIFFRACTION87
1.52-1.540.21521980.20833700X-RAY DIFFRACTION88
1.54-1.560.26371750.21183763X-RAY DIFFRACTION88
1.56-1.590.23751890.20653736X-RAY DIFFRACTION87
1.59-1.610.2441780.20823787X-RAY DIFFRACTION89
1.61-1.640.21842010.19673728X-RAY DIFFRACTION89
1.64-1.670.21751830.1933743X-RAY DIFFRACTION88
1.67-1.70.2261900.19053721X-RAY DIFFRACTION88
1.7-1.740.21111880.19843763X-RAY DIFFRACTION88
1.74-1.780.2121980.1963679X-RAY DIFFRACTION87
1.78-1.820.24722060.19813596X-RAY DIFFRACTION86
1.82-1.860.22921560.19113635X-RAY DIFFRACTION84
1.86-1.910.21711690.1933522X-RAY DIFFRACTION83
1.91-1.970.1921800.19763106X-RAY DIFFRACTION74
1.97-2.030.20321820.18143574X-RAY DIFFRACTION84
2.03-2.110.19321940.17453846X-RAY DIFFRACTION91
2.11-2.190.20782310.1833799X-RAY DIFFRACTION91
2.19-2.290.21462070.18193856X-RAY DIFFRACTION90
2.29-2.410.21222340.17433709X-RAY DIFFRACTION89
2.41-2.560.22181710.1773834X-RAY DIFFRACTION90
2.56-2.760.18961970.17923777X-RAY DIFFRACTION89
2.76-3.040.20522050.17683728X-RAY DIFFRACTION87
3.04-3.480.19281650.17223542X-RAY DIFFRACTION84
3.48-4.380.17881790.15463564X-RAY DIFFRACTION84
4.38-49.30.17432040.16193961X-RAY DIFFRACTION93
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)
11.20790.2398-0.09621.7953-0.2921.4664-0.030.0462-0.0065-0.11740.01690.0402-0.0011-0.11380.00940.12490.01710.00550.098-0.02210.090212.687920.475651.8965
21.31980.2561-0.02851.0659-0.35631.71750.0052-0.00050.05740.02760.0160.0403-0.0715-0.0063-0.00580.06980.00140.0080.0866-0.01470.100426.95785.751617.2593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA25 - 522
2X-RAY DIFFRACTION2chain BB25 - 522

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