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

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Basic information

Entry
Database: PDB / ID: 8dkq
TitleMinimal PutA proline dehydrogenase domain (design #2) complexed with 2-(Furan-2-yl)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 / 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 / DI(HYDROXYETHYL)ETHER / (furan-2-yl)acetic acid / Bifunctional protein PutA
Similarity search - Component
Biological speciesSinorhizobium meliloti SM11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.72 Å
AuthorsTanner, J.J. / Bogner, A.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM132640 United States
CitationJournal: Protein Eng.Des.Sel. / Year: 2022
Title: Structure-based engineering of minimal proline dehydrogenase domains for inhibitor discovery.
Authors: Bogner, A.N. / Ji, J. / Tanner, J.J.
History
DepositionJul 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)89,4777
Polymers87,5482
Non-polymers1,9295
Water8,125451
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Dimer inferred from PDBePISA.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.967, 55.291, 76.092
Angle α, β, γ (deg.)104.070, 100.370, 108.670
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) / Strain: SM11 / Gene: putA, SM11_chr0102 / 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-SJU / (furan-2-yl)acetic acid


Mass: 126.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05 - 0.2 M sodium formate and 19-24% (w/v) PEG 3350

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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 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.72→70.84 Å / Num. obs: 68874 / % possible obs: 92.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 20.53 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.052 / Rrim(I) all: 0.098 / Net I/σ(I): 13.2 / Num. measured all: 247327
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.72-1.750.362921427450.8840.2230.4274.169.2
9.11-70.840.0515324470.9870.0330.0625.588

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.72→49.58 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.15 / Phase error: 19.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1956 3441 5 %
Rwork0.1664 65426 -
obs0.1679 68867 92.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.67 Å2 / Biso mean: 25.5097 Å2 / Biso min: 9.12 Å2
Refinement stepCycle: final / Resolution: 1.72→49.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5822 0 131 451 6404
Biso mean--16.31 29.49 -
Num. residues----769
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.72-1.750.2451100.19011962207269
1.75-1.770.22091530.16952624277793
1.77-1.80.22851300.16792666279694
1.8-1.830.20161340.15892644277894
1.83-1.860.22721490.18072650279994
1.86-1.890.23871510.18682657280894
1.89-1.920.24871530.18692634278794
1.92-1.960.2381380.182708284694
1.96-20.23351540.18262574272893
2-2.040.20221210.17182645276692
2.04-2.090.21481080.16882558266692
2.09-2.140.20681070.17132502260987
2.14-2.20.20551340.18032752288696
2.2-2.270.18991470.17492717286496
2.27-2.340.21951420.17582735287797
2.34-2.420.20791300.17942714284496
2.42-2.520.22361440.17772718286296
2.52-2.630.21231640.1832674283895
2.63-2.770.1921350.17782663279895
2.77-2.950.20231540.17932625277993
2.95-3.170.18981480.17222581272991
3.17-3.490.20471370.1592674281195
3.49-40.17451320.15782634276693
4-5.040.1521270.13272608273592
5.04-49.580.1561390.15332507264689
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)
11.3750.39260.13271.93680.04871.3433-0.0156-0.00840.017-0.0978-0.00520.0705-0.0079-0.13640.0110.12950.03320.00330.1085-0.01010.105511.274920.768652.0095
21.65940.45410.27791.1973-0.16861.7736-0.01690.06320.06690.02070.0120.0616-0.0421-0.02430.00690.0957-0.00090.01440.1162-0.00520.116226.09586.063716.7859
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A')A25 - 522
2X-RAY DIFFRACTION2(chain 'B')B25 - 522

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