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- PDB-3e2q: Crystal Structure Reduced PutA86-630 Mutant Y540S Complexed with ... -

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Basic information

Entry
Database: PDB / ID: 3e2q
TitleCrystal Structure Reduced PutA86-630 Mutant Y540S Complexed with trans-4-hydroxy-L-proline
ComponentsProline dehydrogenase
KeywordsOXIDOREDUCTASE / Proline utilization A / PutA / flavoenzyme / DNA-binding / FAD / Flavoprotein / Multifunctional enzyme / NAD / Proline metabolism / Repressor / Transcription / Transcription regulation
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 / DNA-binding transcription repressor activity / cis-regulatory region sequence-specific DNA binding / cytoplasmic side of plasma membrane / flavin adenine dinucleotide binding ...proline dehydrogenase / proline dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / proline biosynthetic process / DNA-binding transcription repressor activity / cis-regulatory region sequence-specific DNA binding / cytoplasmic side of plasma membrane / flavin adenine dinucleotide binding / response to oxidative stress / sequence-specific DNA binding / negative regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
: / PutA, RHH domain / TIM Barrel - #220 / 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 ...: / PutA, RHH domain / TIM Barrel - #220 / 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 / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 4-HYDROXYPROLINE / Bifunctional protein PutA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å
AuthorsTanner, J.J.
CitationJournal: Biochemistry / Year: 2009
Title: A conserved active site tyrosine residue of proline dehydrogenase helps enforce the preference for proline over hydroxyproline as the substrate.
Authors: Ostrander, E.L. / Larson, J.D. / Schuermann, J.P. / Tanner, J.J.
History
DepositionAug 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proline dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7685
Polymers61,3751
Non-polymers1,3934
Water4,540252
1
A: Proline dehydrogenase
hetero molecules

A: Proline dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,53710
Polymers122,7502
Non-polymers2,7868
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area7670 Å2
ΔGint-50 kcal/mol
Surface area38880 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.080, 141.646, 145.605
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Proline dehydrogenase / Proline oxidase


Mass: 61375.016 Da / Num. of mol.: 1 / Fragment: UNP residues 86-630 / Mutation: Y540S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: putA, poaA / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / References: UniProt: P09546, EC: 1.5.99.8
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-HYP / 4-HYDROXYPROLINE / HYDROXYPROLINE


Type: L-peptide linking / Mass: 131.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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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: 3.07 Å3/Da / Density % sol: 59.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.9
Details: 100 mM citrate buffer, 15-18% PEG 3350, pH 5.9, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2008
RadiationMonochromator: beamline optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 76563 / % possible obs: 99.3 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.047 / Χ2: 0.913
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.75-1.785.50.41837340.59598.5
1.78-1.815.70.36837550.61399.1
1.81-1.855.80.3238060.59599.2
1.85-1.895.80.28937670.60399.2
1.89-1.935.80.2238220.61799.6
1.93-1.975.80.18238010.63899.5
1.97-2.025.80.14338000.6699.6
2.02-2.075.90.12138040.67799.6
2.07-2.145.90.10538210.70699.7
2.14-2.25.90.08938410.72799.7
2.2-2.2860.07738240.77599.9
2.28-2.386.10.06938280.8199.8
2.38-2.486.10.06338250.88999.9
2.48-2.616.10.0638591.024100
2.61-2.786.20.05738731.276100
2.78-2.996.10.05238651.425100
2.99-3.296.10.04238751.387100
3.29-3.775.90.03538951.33899.7
3.77-4.756.10.03239311.38999.7
4.75-505.80.03138371.30493.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.75→40.431 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.843 / SU ML: 0.21 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 3810 4.98 %
Rwork0.201 --
obs0.203 76493 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.899 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso max: 201.92 Å2 / Biso mean: 39.117 Å2 / Biso min: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→40.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3554 0 94 252 3900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063749
X-RAY DIFFRACTIONf_angle_d1.0565092
X-RAY DIFFRACTIONf_chiral_restr0.059564
X-RAY DIFFRACTIONf_plane_restr0.009657
X-RAY DIFFRACTIONf_dihedral_angle_d19.6231406
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.7710.261600.2313268342890
1.771-1.8040.2441770.2123585376299
1.804-1.8380.221700.2083621379199
1.838-1.8760.2511910.2123597378899
1.876-1.9170.2191980.1913635383399
1.917-1.9610.2132070.1883599380699
1.961-2.010.2251950.1943614380999
2.01-2.0650.2322080.19636053813100
2.065-2.1250.2232050.1923632383799
2.125-2.1940.2151920.19136723864100
2.194-2.2720.2261670.18436623829100
2.272-2.3630.1952060.18636433849100
2.363-2.4710.2151860.1936603846100
2.471-2.6010.2362090.19936563865100
2.601-2.7640.2381790.20237093888100
2.764-2.9770.2211990.21336723871100
2.977-3.2770.2331970.20837133910100
3.277-3.7510.2251880.19537113899100
3.751-4.7240.2022010.17737433944100
4.724-40.4420.2541750.2233686386194

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