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- PDB-9c8b: Minimal PutA proline dehydrogenase domain (design #2) with the FA... -

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Basic information

Entry
Database: PDB / ID: 9c8b
TitleMinimal PutA proline dehydrogenase domain (design #2) with the FAD N5 modified with propanal resulting from inactivation with N-allylglycine (replicate #2)
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
PROPANAL / FLAVIN-ADENINE DINUCLEOTIDE / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Bifunctional protein PutA
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.52 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
DepositionJun 12, 2024Deposition 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)91,02310
Polymers87,5482
Non-polymers3,4758
Water8,575476
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.892, 54.954, 76.092
Angle α, β, γ (deg.)104.16, 100.38, 108.65
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bifunctional protein PutA


Mass: 43773.988 Da / Num. of mol.: 2 / Fragment: proline dehydrogenase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: SM11 / Gene: putA, SM11_chr0102 / Production host: Escherichia coli (E. coli)
References: UniProt: F7X6I3, proline dehydrogenase, L-glutamate gamma-semialdehyde dehydrogenase

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Non-polymers , 5 types, 484 molecules

#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-CBG / PROPANAL


Mass: 58.079 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.06 Å3/Da / Density % sol: 40.26 %
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: Apr 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.52→49.25 Å / Num. obs: 99633 / % possible obs: 92.7 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.027 / Rrim(I) all: 0.052 / Net I/σ(I): 13.6 / Num. measured all: 365203
Reflection shellResolution: 1.52→1.55 Å / % possible obs: 90.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.589 / Num. measured all: 17932 / Num. unique obs: 4766 / CC1/2: 0.815 / Rpim(I) all: 0.348 / Rrim(I) all: 0.685 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.52→49.25 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 20.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1906 5008 5.03 %
Rwork0.168 --
obs0.1691 99618 92.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5791 0 234 476 6501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066172
X-RAY DIFFRACTIONf_angle_d0.8888408
X-RAY DIFFRACTIONf_dihedral_angle_d14.4192266
X-RAY DIFFRACTIONf_chiral_restr0.048954
X-RAY DIFFRACTIONf_plane_restr0.0081056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.540.27051540.25293054X-RAY DIFFRACTION90
1.54-1.560.26441550.25093088X-RAY DIFFRACTION90
1.56-1.570.27681870.24123078X-RAY DIFFRACTION91
1.57-1.590.24121480.22543112X-RAY DIFFRACTION91
1.59-1.620.26321600.23613085X-RAY DIFFRACTION91
1.62-1.640.24761750.22193062X-RAY DIFFRACTION90
1.64-1.660.24641790.21013082X-RAY DIFFRACTION91
1.66-1.690.23051810.21133024X-RAY DIFFRACTION89
1.69-1.710.22091660.21132896X-RAY DIFFRACTION86
1.71-1.740.24091380.20052927X-RAY DIFFRACTION85
1.74-1.770.24841860.19223224X-RAY DIFFRACTION95
1.77-1.80.19741690.18473205X-RAY DIFFRACTION95
1.8-1.840.23371670.18213268X-RAY DIFFRACTION95
1.84-1.870.21041650.17743235X-RAY DIFFRACTION95
1.87-1.910.20091920.18063217X-RAY DIFFRACTION95
1.91-1.960.21671610.18773286X-RAY DIFFRACTION95
1.96-2.010.21781720.18893216X-RAY DIFFRACTION95
2.01-2.060.22141500.18083237X-RAY DIFFRACTION95
2.06-2.120.19121570.17553286X-RAY DIFFRACTION95
2.12-2.190.20781600.18113162X-RAY DIFFRACTION94
2.19-2.270.22491770.18133204X-RAY DIFFRACTION94
2.27-2.360.20661710.18333140X-RAY DIFFRACTION92
2.36-2.470.2071360.18063103X-RAY DIFFRACTION91
2.47-2.60.21261880.17823281X-RAY DIFFRACTION96
2.6-2.760.22241820.1733246X-RAY DIFFRACTION96
2.76-2.970.1891450.18183258X-RAY DIFFRACTION95
2.97-3.270.20991730.16873270X-RAY DIFFRACTION95
3.27-3.750.16161860.1493154X-RAY DIFFRACTION93
3.75-4.720.12931300.12793107X-RAY DIFFRACTION91
4.72-49.250.14921980.14053103X-RAY DIFFRACTION92
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)
11.67530.1963-0.00242.1275-0.13511.9764-0.00090.0250.0042-0.2032-0.01350.07370.0657-0.19930.00740.19190.0266-0.00240.167-0.0170.124312.894820.603252.0586
22.30060.58990.31681.4717-0.28612.06440.00350.00420.07820.05860.05460.1217-0.0026-0.1447-0.03790.1168-0.00070.02080.18120.00510.160127.41595.778916.7554
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1peptide and chain A
2X-RAY DIFFRACTION2peptide and chain B

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