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- PDB-4o8a: First structure of a proline utilization A proline dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 4o8a
TitleFirst structure of a proline utilization A proline dehydrogenase domain
ComponentsBifunctional protein PutA
KeywordsOXIDOREDUCTASE / flavoenzyme / proline dehydrogenase / PutA / proline utilization A / aldehyde dehydrogenase
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
(2S)-2-HYDROXYPROPANOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / Bifunctional protein PutA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsTanner, J.J.
Citation
Journal: Nat.Struct.Biol. / Year: 2003
Title: Structure of the proline dehydrogenase domain of the multifunctional PutA flavoprotein.
Authors: Lee, Y.H. / Nadaraia, S. / Gu, D. / Becker, D.F. / Tanner, J.J.
#1: Journal: Nat.Struct.Biol. / Year: 2003
Title: Structure of the proline dehydrogenase domain of the multifunctional PutA flavoprotein.
Authors: Lee, Y.H. / Nadaraia, S. / Gu, D. / Becker, D.F. / Tanner, J.J.
History
DepositionDec 26, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionJan 15, 2014ID: 1K87
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3615
Polymers76,0971
Non-polymers1,2644
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Bifunctional protein PutA
hetero molecules

A: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,72110
Polymers152,1932
Non-polymers2,5288
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area7350 Å2
ΔGint-38 kcal/mol
Surface area38530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.620, 140.430, 145.850
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 Bifunctional protein PutA / Proline dehydrogenase / Proline oxidase / Delta-1-pyrroline-5-carboxylate dehydrogenase / P5C ...Proline dehydrogenase / Proline oxidase / Delta-1-pyrroline-5-carboxylate dehydrogenase / P5C dehydrogenase / L-glutamate gamma-semialdehyde dehydrogenase


Mass: 76096.617 Da / Num. of mol.: 1 / Fragment: residues 1-669
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1014, JW0999, poaA, putA / Plasmid: pet23b / Production host: Escherichia coli (E. coli)
References: UniProt: P09546, EC: 1.5.99.8, L-glutamate gamma-semialdehyde dehydrogenase
#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-2OP / (2S)-2-HYDROXYPROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: PEG 4000, SODIUM CITRATE, pH 6.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.005 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 12, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 2→28.487 Å / Num. all: 50208 / Num. obs: 50208 / % possible obs: 99 % / Redundancy: 5.8 % / Biso Wilson estimate: 32.95 Å2 / Rsym value: 0.06 / Net I/σ(I): 20.1
Reflection shellResolution: 2→2.25 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.7 / % possible all: 97.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PDB_EXTRACT3.14data extraction
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 2→28.487 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8653 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 5047 10.05 %random
Rwork0.1861 ---
obs0.1893 50196 99.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.19 Å2 / Biso mean: 35.6957 Å2 / Biso min: 12.7 Å2
Refinement stepCycle: LAST / Resolution: 2→28.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3528 0 85 204 3817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073695
X-RAY DIFFRACTIONf_angle_d1.0715015
X-RAY DIFFRACTIONf_chiral_restr0.071563
X-RAY DIFFRACTIONf_plane_restr0.004646
X-RAY DIFFRACTIONf_dihedral_angle_d16.2651413
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02270.28511780.26211443162197
2.0227-2.04650.2951530.24011449160298
2.0465-2.07150.29191800.24211508168898
2.0715-2.09770.25561660.23211438160498
2.0977-2.12530.26761680.22341469163798
2.1253-2.15440.29131720.21111488166098
2.1544-2.18510.27111360.21031492162899
2.1851-2.21770.22631730.19381452162598
2.2177-2.25240.24211680.20251492166099
2.2524-2.28930.22921780.18571467164598
2.2893-2.32870.21421700.17481475164599
2.3287-2.37110.23821610.17651473163498
2.3711-2.41660.22521670.17481502166999
2.4166-2.4660.21851760.1761490166699
2.466-2.51950.22251820.18351484166699
2.5195-2.57810.2131490.170415071656100
2.5781-2.64250.20271780.16815081686100
2.6425-2.71390.21061730.171915011674100
2.7139-2.79370.23041540.173515381692100
2.7937-2.88380.22221770.188115011678100
2.8838-2.98680.24281510.192415481699100
2.9868-3.10620.22811780.198815031681100
3.1062-3.24740.20281550.18815461701100
3.2474-3.41840.21831850.196515091694100
3.4184-3.63210.20541630.17515431706100
3.6321-3.91190.20571660.174515401706100
3.9119-4.30440.19351630.149415651728100
4.3044-4.92450.16471510.146615601711100
4.9245-6.19380.20221850.194415581743100
6.1938-28.48980.24661910.23411600179198
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)
11.938-0.5815-0.04161.96430.24522.6301-0.01960.2028-0.2369-0.1158-0.01870.1850.1328-0.2622-0.06090.209-0.0155-0.02470.2853-0.01890.2433-6.156840.153850.5698
21.6761-0.2125-0.17560.7814-0.0561.86410.2230.4108-0.2207-0.8544-0.10510.35570.4362-0.4945-0.11730.9187-0.0449-0.14560.5930.04820.4778-15.020480.971329.3322
31.9411-0.149-0.68131.06660.48162.91630.0930.08190.0232-0.17150.0893-0.1246-0.18620.3413-0.0880.1507-0.02130.02370.1416-0.04620.17458.527746.152353.0375
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 88:142A88 - 142
2X-RAY DIFFRACTION2chain A and resseq 143:184A143 - 184
3X-RAY DIFFRACTION3chain A and resseq 243:610A243 - 610

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