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- PDB-9dl9: Structure of proline utilization A co-crystallized with 4-methoxy... -

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Basic information

Entry
Database: PDB / ID: 9dl9
TitleStructure of proline utilization A co-crystallized with 4-methoxybenzyl alcohol
ComponentsBifunctional protein PutA
KeywordsOXIDOREDUCTASE / FLAVOENZYME / ROSSMANN FOLD / PROLINE DEHYDROGENASE / ALDEHYDE DEHYDROGENASE / PROLINE CATABOLISM / SUBSTRATE CHANNELING / BIFUNCTIONAL ENZYME
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
: / FLAVIN-ADENINE DINUCLEOTIDE / FORMIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Bifunctional protein PutA
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.32 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: Molecules / Year: 2024
Title: Crystallographic Fragment Screening of a Bifunctional Proline Catabolic Enzyme Reveals New Inhibitor Templates for Proline Dehydrogenase and L-Glutamate-gamma-semialdehyde Dehydrogenase.
Authors: Meeks, K.R. / Bogner, A.N. / Nix, J.C. / Tanner, J.J.
History
DepositionSep 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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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)268,95627
Polymers263,9232
Non-polymers5,03325
Water47,9202660
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13600 Å2
ΔGint-124 kcal/mol
Surface area77170 Å2
MethodPISA
2
A: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,36613
Polymers131,9621
Non-polymers2,40412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,59014
Polymers131,9621
Non-polymers2,62813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.745, 101.959, 126.167
Angle α, β, γ (deg.)90.00, 106.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bifunctional protein PutA


Mass: 131961.656 Da / Num. of mol.: 2
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 , 10 types, 2685 molecules

#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-A1BDD / (4-methoxyphenyl)methanol


Mass: 138.164 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2660 / 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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Reservoir contained 0.1 M HEPES, pH 7.5, 0.1 M sodium formate, 0.1 M magnesium chloride, 0.2 M ammonium sulfate, and 18% (w/v) PEG 3350. Enzyme was incubated with 20 mM 4-Methoxybenzyl ...Details: Reservoir contained 0.1 M HEPES, pH 7.5, 0.1 M sodium formate, 0.1 M magnesium chloride, 0.2 M ammonium sulfate, and 18% (w/v) PEG 3350. Enzyme was incubated with 20 mM 4-Methoxybenzyl alcohol. Crystal was soaked in cryobuffer containing 67 mM 4-Methoxybenzyl alcohol and 20% PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00009 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00009 Å / Relative weight: 1
ReflectionResolution: 1.32→48.34 Å / Num. obs: 1056665 / % possible obs: 94.3 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.021 / Rrim(I) all: 0.056 / Χ2: 0.93 / Net I/σ(I): 16.6
Reflection shellResolution: 1.32→1.34 Å / % possible obs: 62.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 1.72 / Num. measured all: 80807 / Num. unique obs: 17661 / CC1/2: 0.352 / Rpim(I) all: 0.886 / Rrim(I) all: 1.942 / Χ2: 0.65 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.32→46.99 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1878 53398 5.05 %
Rwork0.1682 --
obs0.1692 1056665 93.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.32→46.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17891 0 330 2660 20881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618989
X-RAY DIFFRACTIONf_angle_d0.96125948
X-RAY DIFFRACTIONf_dihedral_angle_d16.8247160
X-RAY DIFFRACTIONf_chiral_restr0.0713038
X-RAY DIFFRACTIONf_plane_restr0.0083357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.340.367710970.337221185X-RAY DIFFRACTION59
1.34-1.350.327511580.327223403X-RAY DIFFRACTION65
1.35-1.370.34813240.317625458X-RAY DIFFRACTION71
1.37-1.380.32415740.303627669X-RAY DIFFRACTION77
1.38-1.40.302815230.295329953X-RAY DIFFRACTION83
1.4-1.420.30317800.286232233X-RAY DIFFRACTION90
1.42-1.440.294818200.269635077X-RAY DIFFRACTION98
1.44-1.460.279919890.252535703X-RAY DIFFRACTION99
1.46-1.490.252318960.244535442X-RAY DIFFRACTION99
1.49-1.510.260320280.231335440X-RAY DIFFRACTION99
1.51-1.540.241418760.214535617X-RAY DIFFRACTION99
1.54-1.570.227519220.206835493X-RAY DIFFRACTION99
1.57-1.60.218319180.198935446X-RAY DIFFRACTION99
1.6-1.630.223918060.192535551X-RAY DIFFRACTION99
1.63-1.660.214818710.184535202X-RAY DIFFRACTION98
1.66-1.70.207319420.181535251X-RAY DIFFRACTION98
1.7-1.740.209517260.180835337X-RAY DIFFRACTION98
1.74-1.790.201417760.183235138X-RAY DIFFRACTION98
1.79-1.840.217819390.19234546X-RAY DIFFRACTION97
1.84-1.90.223518440.186333440X-RAY DIFFRACTION93
1.9-1.970.194318980.175435041X-RAY DIFFRACTION98
1.97-2.050.190217670.167235717X-RAY DIFFRACTION99
2.05-2.140.18419140.163335469X-RAY DIFFRACTION99
2.14-2.260.183418710.160335274X-RAY DIFFRACTION98
2.26-2.40.18219910.158835273X-RAY DIFFRACTION99
2.4-2.580.176118540.160435302X-RAY DIFFRACTION98
2.58-2.840.177818800.160635118X-RAY DIFFRACTION98
2.84-3.260.173216980.157434304X-RAY DIFFRACTION95
3.26-4.10.157617490.137533515X-RAY DIFFRACTION93
4.1-46.990.147519670.134735670X-RAY DIFFRACTION100
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)
10.6121-0.01230.17940.0946-0.00410.1283-0.0354-0.11180.01040.02930.03370.0145-0.019-0.02050.00160.15250.01980.01210.13140.00630.1243-25.544565.914992.7467
20.17410.00890.03740.2092-0.05770.29980.0087-0.0284-0.00320.04080.0017-0.00560.021-0.0591-0.01370.11940.004-0.00260.1297-0.01730.11915.773431.191891.5254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and peptide
2X-RAY DIFFRACTION2chain B and peptide

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