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- PDB-2fzn: Structure of the E. coli PutA proline dehydrogenase domain reduce... -

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Basic information

Entry
Database: PDB / ID: 2fzn
TitleStructure of the E. coli PutA proline dehydrogenase domain reduced by dithionite and complexed with proline
ComponentsBifunctional protein putA, Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase)
KeywordsOXIDOREDUCTASE / proline utilization A / proline dehydrogenase / PutA / flavoenzyme / proline catabolism / dithionite-reduced
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 / sequence-specific DNA binding / response to oxidative stress / negative regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Single helix bin / : / 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 ...Single helix bin / : / 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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PROLINE / Bifunctional protein PutA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTanner, J.J.
CitationJournal: To be Published
Title: Hydrogen Bonding Interactions of the 2-OH Ribityl Group and the N(5) Position of the FAD Cofactor Regulate PutA-membrane Associations in Escherichia coli
Authors: Zhang, W. / Zhang, M. / Zhu, W. / Wanduragula, S. / Rewinkel, D. / Tanner, J.J. / Becker, D.F.
History
DepositionFeb 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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, Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5693
Polymers66,6681
Non-polymers9012
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Bifunctional protein putA, Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase)
hetero molecules

A: Bifunctional protein putA, Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,1386
Polymers133,3362
Non-polymers1,8014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area6260 Å2
ΔGint-49 kcal/mol
Surface area37750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.115, 143.221, 145.124
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThis protein (PutA86-669) corresponds to residues 86-669 of full-length E. coli Proline Utilization A (PutA). PutA is a dimer in solution, but PutA86-669 is monomeric. The asymmetric unit contains 1 PutA86-669 monomer.

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Components

#1: Protein Bifunctional protein putA, Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase)


Mass: 66668.070 Da / Num. of mol.: 1 / Fragment: Residues 86-669
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: putA / Plasmid: pUTA669 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / 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-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.85 Å3/Da / Density % sol: 56.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: The crystal was grown in 13-15% PEG 3350, 60-190 mM citrate buffer. Prior to data collection a crystal was soaked in excess Na dithionite and proline in order to reduce the FAD cofactor., pH ...Details: The crystal was grown in 13-15% PEG 3350, 60-190 mM citrate buffer. Prior to data collection a crystal was soaked in excess Na dithionite and proline in order to reduce the FAD cofactor., pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97856 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→27 Å / Num. obs: 51335 / % possible obs: 98.1 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.061 / Χ2: 1.004 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID
2-2.0791.24.70.41947061.0181
2.07-2.1597.55.20.37350541.0011
2.15-2.2599.95.60.29551481.0161
2.25-2.3799.95.90.22751941.0051
2.37-2.5210060.17452061.0071
2.52-2.7110060.12252120.9991
2.71-2.9910060.0851920.9891
2.99-3.4210060.05152630.9931
3.42-4.399.65.80.03752851.0041
4.3-27935.50.02950751.0181

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1TJ0

1tj0


Resolution: 2→22.7 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.696 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2508 5 %RANDOM
Rwork0.214 ---
all0.216 ---
obs0.216 49878 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.509 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2--4.87 Å20 Å2
3----4.1 Å2
Refinement stepCycle: LAST / Resolution: 2→22.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3460 0 61 183 3704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213590
X-RAY DIFFRACTIONr_bond_other_d0.0020.023298
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9954875
X-RAY DIFFRACTIONr_angle_other_deg0.83437611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4255446
X-RAY DIFFRACTIONr_chiral_restr0.0790.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023988
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02716
X-RAY DIFFRACTIONr_nbd_refined0.2090.2771
X-RAY DIFFRACTIONr_nbd_other0.2430.23864
X-RAY DIFFRACTIONr_nbtor_other0.0850.22005
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2178
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.26
X-RAY DIFFRACTIONr_mcbond_it0.7331.52236
X-RAY DIFFRACTIONr_mcangle_it1.3223558
X-RAY DIFFRACTIONr_scbond_it2.15731354
X-RAY DIFFRACTIONr_scangle_it3.4584.51317
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.274 193
Rwork0.273 3258
obs-3451
Refinement TLS params.Method: refined / Origin x: 7.051 Å / Origin y: 45.959 Å / Origin z: 52.312 Å
111213212223313233
T0.1253 Å2-0.0065 Å20.0076 Å2-0.0058 Å2-0.0302 Å2--0.1635 Å2
L1.2262 °2-0.0255 °2-0.4451 °2-0.2816 °2-0.0063 °2--2.6175 °2
S0.0803 Å °0.0865 Å °0.0099 Å °-0.0311 Å °0.0574 Å °0.0052 Å °-0.1722 Å °0.1258 Å °-0.1377 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDAuth seq-IDLabel seq-ID
188 - 1463 - 61
2244 - 610159 - 525

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