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

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Basic information

Entry
Database: PDB / ID: 8dkp
TitleMinimal PutA proline dehydrogenase domain (design #2) complexed with S-(-)-tetrahydro-2-furoic 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
TIM Barrel - #220 / 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 ...TIM Barrel - #220 / 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 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / TETRAHYDROFURAN-2-CARBOXYLIC ACID / Bifunctional protein PutA
Similarity search - Component
Biological speciesSinorhizobium meliloti SM11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 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 1.2Oct 25, 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)89,3516
Polymers87,5482
Non-polymers1,8034
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Dimer inferred from PDBePISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-37 kcal/mol
Surface area29610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.839, 55.130, 75.947
Angle α, β, γ (deg.)103.990, 100.390, 108.460
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-TFB / TETRAHYDROFURAN-2-CARBOXYLIC ACID


Mass: 116.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.06 Å3/Da / Density % sol: 40.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium formate and 20% (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: 1.23→70.76 Å / Num. obs: 179731 / % possible obs: 88.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 15.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.022 / Rrim(I) all: 0.042 / Net I/σ(I): 18.5 / Num. measured all: 658243
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.23-1.253.80.2992819375120.9460.1770.3483.674.4
6.73-70.763.60.045409111440.9930.0280.05441.992

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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: MOLECULAR REPLACEMENT
Starting model: 6X9A

6x9a


Resolution: 1.23→70.76 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.15 / Phase error: 19.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1844 8725 4.86 %
Rwork0.1737 170975 -
obs0.1743 179700 88.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.95 Å2 / Biso mean: 22.379 Å2 / Biso min: 9.37 Å2
Refinement stepCycle: final / Resolution: 1.23→70.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5886 0 122 552 6560
Biso mean--12.23 26.15 -
Num. residues----774
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.23-1.240.24732160.23594730494673
1.24-1.260.22122440.23254975521977
1.26-1.270.22122550.22815249550481
1.27-1.290.24442730.225428570183
1.29-1.310.24122520.21825417566984
1.31-1.320.21282750.21265375565083
1.32-1.340.23622530.20115387564083
1.34-1.360.2182800.20255333561383
1.36-1.380.20642890.20135431572084
1.38-1.410.21182600.19795538579885
1.41-1.430.21873050.19545441574685
1.43-1.460.20762980.19165267556581
1.46-1.490.20083030.1885424572784
1.49-1.520.19373020.18995804610690
1.52-1.550.21473220.18735881620391
1.55-1.580.19662970.17916005630292
1.58-1.620.20373050.17956147645294
1.62-1.670.18173040.17345948625293
1.67-1.720.19112740.17816087636194
1.72-1.770.18653100.17646064637494
1.77-1.840.19993060.18276072637893
1.84-1.910.20893020.1845967626992
1.91-20.19822710.18155650592188
2-2.10.16723080.17356130643894
2.1-2.230.19883260.17436106643294
2.23-2.410.19233380.17166063640195
2.41-2.650.18082750.17836114638994
2.65-3.030.19343360.17585953628993
3.03-3.820.16093210.16415919624092
3.82-70.760.15693250.14616070639594
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)
10.98580.3404-0.1161.9907-0.37591.4859-0.03720.04030.011-0.11690.05410.07-0.0213-0.1492-0.01140.12330.02410.00240.0952-0.01230.084711.796820.35851.9868
21.15430.3464-0.10281.3161-0.40831.60140.00310.00970.03660.01230.0020.0577-0.0528-0.00340.00580.05780.00070.00080.0876-0.0070.084525.93075.714816.9217
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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