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- PDB-7na0: Structure of Geobacter sulfurreducens proline utilization A (PutA... -

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Basic information

Entry
Database: PDB / ID: 7na0
TitleStructure of Geobacter sulfurreducens proline utilization A (PutA) variant A206W
ComponentsBifunctional protein PutA
KeywordsOXIDOREDUCTASE / FLAVOENZYME / ROSSMANN FOLD / ALDEHYDE DEHYDROGENASE / PROLINE CATABOLISM / SUBSTRATE CHANNELING / BIFUNCTIONAL ENZYME
Function / homology
Function and homology information


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
Similarity search - Function
Proline utilization A, N-terminal / Proline utilization A N-terminal domain / 1-pyrroline-5-carboxylate dehydrogenase / Bifunctional protein PutA / Proline dehydrogenase domain / Proline dehydrogenase / : / FAD-linked oxidoreductase-like / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. ...Proline utilization A, N-terminal / Proline utilization A N-terminal domain / 1-pyrroline-5-carboxylate 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 / L-glutamate gamma-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsTanner, J.J. / Korasick, D.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM065546 United States
CitationJournal: Arch.Biochem.Biophys. / Year: 2021
Title: Probing the function of a ligand-modulated dynamic tunnel in bifunctional proline utilization A (PutA).
Authors: Korasick, D.A. / Christgen, S.L. / Qureshi, I.A. / Becker, D.F. / Tanner, J.J.
History
DepositionJun 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 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

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)229,93858
Polymers224,8802
Non-polymers5,05956
Water26,3381462
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22170 Å2
ΔGint40 kcal/mol
Surface area66890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.418, 151.382, 175.553
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bifunctional protein PutA


Mass: 112439.805 Da / Num. of mol.: 2 / Mutation: A206W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA) (bacteria)
Strain: ATCC 51573 / DSM 12127 / PCA / Gene: putA, GSU3395 / Production host: Escherichia coli (E. coli)
References: UniProt: Q746X3, 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1462 / 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: 2.82 Å3/Da / Density % sol: 56.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 M ammonium sulfate, 0.05 M BIS-TRIS pH 6.5, and 30% (v/v) pentaerythritol ethoxylate (15/4 EO/OH)

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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: Feb 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→58.52 Å / Num. obs: 386519 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.057 / Rrim(I) all: 0.152 / Net I/σ(I): 13.4
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
1.9-1.936.61.0026487697870.7620.4211.0882100
10.41-58.526.70.028920613790.9990.0120.03145.499.2

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHENIX1.14refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4NM9

4nm9


Resolution: 1.9→56.181 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.29 / Phase error: 19.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1986 19457 5.03 %
Rwork0.1688 367062 -
obs0.1703 199837 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.17 Å2 / Biso mean: 21.4417 Å2 / Biso min: 7.68 Å2
Refinement stepCycle: final / Resolution: 1.9→56.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15336 0 326 1462 17124
Biso mean--26.37 27.2 -
Num. residues----1959
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.92160.33915910.29221221099
1.9216-1.94420.3156400.274112292100
1.9442-1.96790.28076730.253112140100
1.9679-1.99280.27716630.23812270100
1.9928-2.0190.2716400.230312204100
2.019-2.04670.25016630.221312234100
2.0467-2.0760.27156610.220512233100
2.076-2.10690.23996670.207412208100
2.1069-2.13990.23066350.194912203100
2.1399-2.17490.23866270.198312311100
2.1749-2.21240.21996040.188812251100
2.2124-2.25270.20656220.188212249100
2.2527-2.2960.23236080.179812314100
2.296-2.34290.19846870.166312194100
2.3429-2.39380.19326820.160612165100
2.3938-2.44950.20276160.166912305100
2.4495-2.51080.20386110.163712323100
2.5108-2.57870.22016190.161812223100
2.5787-2.65450.19346140.15312335100
2.6545-2.74020.18436370.149112208100
2.7402-2.83810.18746820.151212203100
2.8381-2.95180.19726530.159912204100
2.9518-3.08610.17426840.16112276100
3.0861-3.24880.19066050.154612229100
3.2488-3.45230.18347050.155912202100
3.4523-3.71880.16266620.148312194100
3.7188-4.0930.15296930.135712205100
4.093-4.6850.15846660.129812222100
4.685-5.90150.17027270.147512175100
5.9015-56.1810.1776200.155812280100
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)
10.4847-0.0202-0.0270.11750.06510.3078-0.00750.08970.0335-0.00520.0108-0.0319-0.01520.0841-0.00940.11260.0025-0.01710.11940.00310.102951.2045-4.91071.0592
20.1135-0.0301-0.02250.26620.12980.349-0.00140.01710.0427-0.0015-0.00440.0024-0.0532-0.00890.00420.0979-0.0029-0.00840.10460.00170.110512.434324.831438.8359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(peptide and chain 'A' )A0
2X-RAY DIFFRACTION2(peptide and chain 'B' )B0

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