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- PDB-6x9c: Structure of proline utilization A with L-proline bound in the L-... -

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Basic information

Entry
Database: PDB / ID: 6x9c
TitleStructure of proline utilization A with L-proline bound in the L-glutamate-gamma-semialdehyde dehydrogenase active site
ComponentsBifunctional protein PutA
KeywordsOXIDOREDUCTASE / FLAVOENZYME / ROSSMANN FOLD / PROLINE DEHYDROGNEASE / ALDEHYDE DEHYDROGENASE / PROLINE CATABOLISM / SUBSTRATE CHANNELING / BIFUNCTIONAL ENZYME
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; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / FORMIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PROLINE / Bifunctional protein PutA
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.44 Å
AuthorsTanner, J.J. / Campbell, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM065546 United States
CitationJournal: Arch.Biochem.Biophys. / Year: 2020
Title: Structural analysis of prolines and hydroxyprolines binding to the l-glutamate-gamma-semialdehyde dehydrogenase active site of bifunctional proline utilization A.
Authors: Campbell, A.C. / Bogner, A.N. / Mao, Y. / Becker, D.F. / Tanner, J.J.
History
DepositionJun 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)268,00619
Polymers263,9232
Non-polymers4,08317
Water35,8861992
1
A: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,11011
Polymers131,9621
Non-polymers2,14810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,8968
Polymers131,9621
Non-polymers1,9357
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10430 Å2
ΔGint-123 kcal/mol
Surface area78460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.079, 102.253, 127.124
Angle α, β, γ (deg.)90.000, 106.480, 90.000
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 (strain SM11) (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 , 9 types, 2009 molecules

#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: 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
#6: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#8: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1992 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Crystallization experiments were set up with SmPutA (6 mg/mL) and NADH (10 mM) in a buffer containing 50 mM Tris (pH 8.0), 50 mM NaCl, 5% (w/v) glycerol, and 0.5 mM Tris(2-caboxyethyl) ...Details: Crystallization experiments were set up with SmPutA (6 mg/mL) and NADH (10 mM) in a buffer containing 50 mM Tris (pH 8.0), 50 mM NaCl, 5% (w/v) glycerol, and 0.5 mM Tris(2-caboxyethyl)phosphine. Crystals were grown using a reservoir solution containing 19% PEG-3350, 0.2 M ammonium sulfate, 0.1 M magnesium chloride, 0.1 M HEPES (pH 8.0), and 0.1 M sodium formate. Cryobuffer: reservoir supplemented with 15 % PEG-200 and 50 mM L-proline

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→48.463 Å / Num. obs: 412199 / % possible obs: 92.4 % / Redundancy: 3.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.036 / Rrim(I) all: 0.069 / Net I/σ(I): 10.9
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
1.44-1.463.31.26344356133290.3650.811.5060.860.4
7.89-48.463.50.024867224950.9980.0150.02933.988.2

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
Aimless0.6.3data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5kf6

5kf6


Resolution: 1.44→48.46 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 22.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2053 20726 5.04 %
Rwork0.1798 390540 -
obs0.1811 411266 92.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.09 Å2 / Biso mean: 25.7581 Å2 / Biso min: 7.72 Å2
Refinement stepCycle: final / Resolution: 1.44→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17842 0 309 1992 20143
Biso mean--25.7 31.6 -
Num. residues----2417
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.44-1.45640.34594520.324817558
1.4564-1.47350.31814770.3082892764
1.4735-1.49150.32144640.3004990470
1.4915-1.51040.30836180.28081074376
1.5104-1.53020.29786470.27231195785
1.5302-1.55120.28057360.2621340495
1.5512-1.57340.27667310.25241346296
1.5734-1.59680.26756990.24251353496
1.5968-1.62180.26177490.23811346296
1.6218-1.64840.25866860.22991362596
1.6484-1.67680.24446630.21731358896
1.6768-1.70730.24097560.21261360696
1.7073-1.74010.23156880.20991364797
1.7401-1.77570.23987280.20471366297
1.7757-1.81430.23027370.20521367497
1.8143-1.85650.23717450.20071366897
1.8565-1.90290.23987270.20631371397
1.9029-1.95440.21947730.19721365597
1.9544-2.01190.22977430.19061375997
2.0119-2.07680.22537450.18971371797
2.0768-2.1510.21287220.18751375797
2.151-2.23720.21946910.18031378297
2.2372-2.3390.20887080.17831374497
2.339-2.46230.21527220.17681373097
2.4623-2.61650.21067450.17621373697
2.6165-2.81850.18517100.17341369396
2.8185-3.10210.20027640.17271352296
3.1021-3.55090.18496960.16511342594
3.5509-4.47330.16126910.13771352495
4.4733-48.4630.1537130.14271374595
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)
10.6462-0.0580.17620.1279-0.02770.1835-0.0413-0.07820.00560.04160.04540.0216-0.0197-0.0282-0.00450.1420.01310.01540.10710.01380.1148-26.133866.029493.5436
20.2721-0.01980.12170.2815-0.06310.48440.0191-0.0317-0.02350.0510.0215-0.01120.0674-0.0869-0.03850.11570.0051-0.0060.1297-0.01510.1185.393431.121892.0437
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A')A0
2X-RAY DIFFRACTION2(chain 'B')B0

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