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- PDB-8dko: Minimal PutA proline dehydrogenase domain (design #1) complexed w... -

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Basic information

Entry
Database: PDB / ID: 8dko
TitleMinimal PutA proline dehydrogenase domain (design #1) 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 / 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 / TETRAHYDROFURAN-2-CARBOXYLIC ACID / Bifunctional protein PutA
Similarity search - Component
Biological speciesSinorhizobium meliloti SM11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

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Assembly

Deposited unit
A: Bifunctional protein PutA
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6136
Polymers90,8102
Non-polymers1,8034
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Based on analysis with PDBePISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-37 kcal/mol
Surface area29690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.980, 54.232, 76.191
Angle α, β, γ (deg.)104.020, 100.500, 108.860
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Bifunctional protein PutA


Mass: 45404.957 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.: 268 / 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: 1.96 Å3/Da / Density % sol: 37.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M potassium thiocyanate and 25% (w/v) PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→47.94 Å / Num. obs: 59009 / % possible obs: 92.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 27.82 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.062 / Rrim(I) all: 0.119 / Net I/σ(I): 7.3 / Num. measured all: 216976 / Scaling rejects: 707
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.8 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.840.6661329235030.8020.3920.7731.793.1
9-47.940.06117714660.9920.0360.07117.690.5

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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: 1.8→47.94 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 1127 1.91 %
Rwork0.1818 57806 -
obs0.1826 58933 92.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.25 Å2 / Biso mean: 34.9098 Å2 / Biso min: 13.41 Å2
Refinement stepCycle: final / Resolution: 1.8→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5825 0 122 268 6215
Biso mean--23.26 34.91 -
Num. residues----777
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.880.30951400.2667340748093
1.88-1.980.27951360.25067078721491
1.98-2.110.25861560.21477099725590
2.11-2.270.27311320.21247292742493
2.27-2.50.26571590.19467421758095
2.5-2.860.24451390.19397309744893
2.86-3.60.21691230.18037229735292
3.6-47.940.17421420.14577038718090
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)
11.71790.10940.24291.5294-0.0261.8892-0.0214-0.02290.0399-0.1089-0.02070.03530.0302-0.20250.03430.22590.05010.01630.1909-0.01850.146912.232720.994352.0883
21.98040.52570.85931.59650.3412.18980.0411-0.05460.00930.1475-0.00970.06550.0765-0.2618-0.0280.1998-0.00520.03240.17870.00380.151826.52456.501516.7643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA25 - 538
2X-RAY DIFFRACTION2chain BB25 - 538

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