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- PDB-8w0k: Minimal PutA proline dehydrogenase domain (design #2) complexed w... -

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Basic information

Entry
Database: PDB / ID: 8w0k
TitleMinimal PutA proline dehydrogenase domain (design #2) complexed with 1-hydroxyethane-1-sulfonate
ComponentsBifunctional protein PutA fusion protein
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 / : / 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 / : / Bifunctional protein PutA
Similarity search - Component
Biological speciesSinorhizobium meliloti SM11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.42 Å
AuthorsTanner, J.J. / Meeks, K.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132640 United States
CitationJournal: Protein Sci. / Year: 2024
Title: Screening a knowledge-based library of low molecular weight compounds against the proline biosynthetic enzyme 1-pyrroline-5-carboxylate 1 (PYCR1).
Authors: Meeks, K.R. / Bogner, A.N. / Tanner, J.J.
History
DepositionFeb 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)89,3716
Polymers87,5482
Non-polymers1,8234
Water9,116506
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.872, 55.060, 76.077
Angle α, β, γ (deg.)104.18, 100.25, 108.26
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Bifunctional protein PutA fusion protein


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 / 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-GHO / (1R)-1-hydroxyethane-1-sulfonic acid


Mass: 126.132 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 2.07 Å3/Da / Density % sol: 40.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir contained 0.2 M sodium formate and 20% (w/v) PEG 3350. Enzyme solution contained 20 mM 1-hydroxyethane-1-sulfonate. Crystal was soaked in cryobuffer containing 20% PEG 200 and 20 ...Details: Reservoir contained 0.2 M sodium formate and 20% (w/v) PEG 3350. Enzyme solution contained 20 mM 1-hydroxyethane-1-sulfonate. Crystal was soaked in cryobuffer containing 20% PEG 200 and 20 mM 1-hydroxyethane-1-sulfonate

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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: Apr 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.42→49.5 Å / Num. obs: 226093 / % possible obs: 88.7 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.026 / Rrim(I) all: 0.05 / Net I/σ(I): 14.6
Reflection shellResolution: 1.42→1.44 Å / % possible obs: 57.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.52 / Num. measured all: 14268 / Num. unique obs: 3812 / CC1/2: 0.823 / Rpim(I) all: 0.307 / Rrim(I) all: 0.604 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5156: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.42→49.5 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 21.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1928 10954 4.84 %
Rwork0.1706 --
obs0.1716 226093 85.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5689 0 120 506 6315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065974
X-RAY DIFFRACTIONf_angle_d0.9598148
X-RAY DIFFRACTIONf_dihedral_angle_d14.832194
X-RAY DIFFRACTIONf_chiral_restr0.071934
X-RAY DIFFRACTIONf_plane_restr0.0071042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.27022250.28544614X-RAY DIFFRACTION55
1.44-1.450.27772640.26545305X-RAY DIFFRACTION62
1.45-1.470.30873060.24895774X-RAY DIFFRACTION70
1.47-1.490.23153170.2297058X-RAY DIFFRACTION83
1.49-1.510.23393620.21736990X-RAY DIFFRACTION84
1.51-1.530.25583650.21137326X-RAY DIFFRACTION86
1.53-1.550.22493540.20317374X-RAY DIFFRACTION89
1.55-1.570.20713710.20047595X-RAY DIFFRACTION89
1.57-1.60.23133720.19967477X-RAY DIFFRACTION90
1.6-1.630.233630.19977590X-RAY DIFFRACTION90
1.63-1.650.22143830.19387449X-RAY DIFFRACTION89
1.65-1.680.20553720.19177611X-RAY DIFFRACTION90
1.68-1.720.2183940.20477500X-RAY DIFFRACTION90
1.72-1.750.22923920.21457453X-RAY DIFFRACTION89
1.75-1.790.24183830.21337267X-RAY DIFFRACTION87
1.79-1.830.23093690.20437121X-RAY DIFFRACTION85
1.83-1.880.21593640.19477813X-RAY DIFFRACTION93
1.88-1.930.23843890.1957750X-RAY DIFFRACTION93
1.93-1.980.20294040.19267740X-RAY DIFFRACTION92
1.98-2.050.19984040.19237777X-RAY DIFFRACTION92
2.05-2.120.19694030.18237645X-RAY DIFFRACTION90
2.12-2.210.21754120.18567347X-RAY DIFFRACTION89
2.21-2.310.19354250.17957336X-RAY DIFFRACTION88
2.31-2.430.20324190.17787267X-RAY DIFFRACTION87
2.43-2.580.21623180.17526887X-RAY DIFFRACTION82
2.58-2.780.18963710.17297245X-RAY DIFFRACTION86
2.78-3.060.19023870.177187X-RAY DIFFRACTION85
3.06-3.50.18093320.15257089X-RAY DIFFRACTION85
3.5-4.410.15683530.13687258X-RAY DIFFRACTION86
4.41-49.50.15893810.14157294X-RAY DIFFRACTION87

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