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- PDB-1tj2: Crystal structure of E. coli PutA proline dehydrogenase domain (r... -

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Basic information

Entry
Database: PDB / ID: 1tj2
TitleCrystal structure of E. coli PutA proline dehydrogenase domain (residues 86-669) complexed with acetate
ComponentsBifunctional putA protein
KeywordsOXIDOREDUCTASE / beta/alpha barrel / flavoenzyme / FAD / proline catabolism
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
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, N-terminal / Aldehyde dehydrogenase, C-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
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / Bifunctional protein PutA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsTanner, J.J. / Zhang, M. / White, T.A. / Schuermann, J.P. / Baban, B.A. / Becker, D.F.
Citation
Journal: Biochemistry / Year: 2004
Title: Structures of the Escherichia coli PutA proline dehydrogenase domain in complex with competitive inhibitors
Authors: Zhang, M. / White, T.A. / Schuermann, J.P. / Baban, B.A. / Becker, D.F. / Tanner, J.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Detection of L-lactate in polyethylene glycol solutions confirms the identity of the active-site ligand in a proline dehydrogenase structure
Authors: Zhang, M. / Tanner, J.J.
History
DepositionJun 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 putA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5103
Polymers64,6661
Non-polymers8452
Water3,477193
1


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

A: Bifunctional putA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,0216
Polymers129,3322
Non-polymers1,6894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area6260 Å2
ΔGint-51 kcal/mol
Surface area37550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.855, 141.093, 145.428
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Bifunctional putA protein


Mass: 64665.871 Da / Num. of mol.: 1
Fragment: E. coli PutA proline dehydrogenase domain (residues 86-669)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PUTA, POAA, B1014 / Plasmid: pET-23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: P09546, EC: 1.5.99.8
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 13-15 % PEG 3350, 60-190 mM citrate buffer, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97856 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 15, 2003 / Details: APS 19ID
RadiationMonochromator: APS 19ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.05→99 Å / Num. all: 46790 / Num. obs: 45470 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 14
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4232 / Rsym value: 0.405 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1k87

1k87
PDB Unreleased entry


Resolution: 2.05→22.7 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.693 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.158 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25015 2223 4.9 %RANDOM
Rwork0.20837 ---
all0.21 46790 --
obs0.21034 45470 97 %-
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: 27.081 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--3.31 Å20 Å2
3----3.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.05→22.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3477 0 57 193 3727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213602
X-RAY DIFFRACTIONr_bond_other_d0.0020.023308
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9934889
X-RAY DIFFRACTIONr_angle_other_deg0.82937641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6495447
X-RAY DIFFRACTIONr_chiral_restr0.0790.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024007
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02717
X-RAY DIFFRACTIONr_nbd_refined0.2060.2811
X-RAY DIFFRACTIONr_nbd_other0.2370.23906
X-RAY DIFFRACTIONr_nbtor_other0.0830.22073
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2186
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.210
X-RAY DIFFRACTIONr_mcbond_it0.7231.52234
X-RAY DIFFRACTIONr_mcangle_it1.32723558
X-RAY DIFFRACTIONr_scbond_it2.1531368
X-RAY DIFFRACTIONr_scangle_it3.4664.51331
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 133 -
Rwork0.253 2458 -
obs-2458 91 %
Refinement TLS params.Method: refined / Origin x: 6.827 Å / Origin y: 45.312 Å / Origin z: 52.439 Å
111213212223313233
T0.0599 Å20.0018 Å20.0184 Å2-0.0155 Å2-0.0388 Å2--0.1061 Å2
L0.8361 °20.0352 °2-0.636 °2-0.0872 °20.0689 °2--2.7869 °2
S0.1214 Å °0.0449 Å °-0.0124 Å °-0.0246 Å °0.0927 Å °0.0142 Å °-0.1863 Å °0.1411 Å °-0.2141 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA88 - 1473 - 62
2X-RAY DIFFRACTION1AA244 - 610159 - 525

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