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- PDB-4jnz: Crystal structure of PutA86-630 mutant D370N complexed with L-Tet... -

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Basic information

Entry
Database: PDB / ID: 4jnz
TitleCrystal structure of PutA86-630 mutant D370N complexed with L-Tetrahydro-2-furoic acid
ComponentsBifunctional protein PutA
KeywordsOXIDOREDUCTASE / BETA/ALPHA BARREL / FLAVOENZYME / 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
: / 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 / TETRAHYDROFURAN-2-CARBOXYLIC ACID / Bifunctional protein PutA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.851 Å
AuthorsTanner, J.J.
CitationJournal: Biochemistry / Year: 2013
Title: Involvement of the beta 3-alpha 3 Loop of the Proline Dehydrogenase Domain in Allosteric Regulation of Membrane Association of Proline Utilization A.
Authors: Zhu, W. / Haile, A.M. / Singh, R.K. / Larson, J.D. / Smithen, D. / Chan, J.Y. / Tanner, J.J. / Becker, D.F.
History
DepositionMar 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 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 1.2Sep 20, 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

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Assembly

Deposited unit
A: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0455
Polymers66,6671
Non-polymers1,3784
Water4,648258
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)136,09110
Polymers133,3342
Non-polymers2,7568
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area10150 Å2
ΔGint-85 kcal/mol
Surface area40350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.797, 140.549, 146.951
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 dehydrogenase


Mass: 66667.086 Da / Num. of mol.: 1 / Fragment: residues 86-630 / Mutation: D370N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: putA, poaA, b1014, JW0999 / Production host: Escherichia coli (E. coli) / References: UniProt: P09546, EC: 1.5.99.8, EC: 1.5.1.12
#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-TFB / TETRAHYDROFURAN-2-CARBOXYLIC ACID


Mass: 116.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O3
#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.: 258 / 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: 2.82 Å3/Da / Density % sol: 56.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 11 - 26 % (w/v) PEG 3350 and 0.1 M sodium citrate buffer, 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: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 64199 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.059 / Χ2: 1.24 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.927.30.41763410.7061100
1.92-1.997.40.29663700.7611100
1.99-2.087.40.20763680.8991100
2.08-2.197.40.16763821.0241100
2.19-2.337.40.13163691.2181100
2.33-2.517.30.10964211.3811100
2.51-2.767.30.09663961.7641100
2.76-3.167.30.07564612.0511100
3.16-3.997.10.04564751.6691100
3.99-507.20.02666160.947198.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E2R

3e2r


Resolution: 1.851→40.64 Å / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.8408 / SU ML: 0.14 / σ(F): 1.33 / Phase error: 22.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2245 3233 5.04 %
Rwork0.1924 --
obs0.194 64135 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.15 Å2 / Biso mean: 37.2924 Å2 / Biso min: 13.24 Å2
Refinement stepCycle: LAST / Resolution: 1.851→40.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3709 0 87 258 4054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073890
X-RAY DIFFRACTIONf_angle_d1.0795290
X-RAY DIFFRACTIONf_chiral_restr0.069602
X-RAY DIFFRACTIONf_plane_restr0.004678
X-RAY DIFFRACTIONf_dihedral_angle_d16.5041459
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.851-1.87870.29621130.22992478259193
1.8787-1.9080.24331490.211426472796100
1.908-1.93930.27971590.197625712730100
1.9393-1.97270.2311430.202126362779100
1.9727-2.00860.23931490.199226192768100
2.0086-2.04730.20851520.193426292781100
2.0473-2.0890.2141500.193526252775100
2.089-2.13450.22611420.197526382780100
2.1345-2.18410.25621430.189326102753100
2.1841-2.23870.21991200.190526652785100
2.2387-2.29930.24391310.199626782809100
2.2993-2.36690.17931470.189626232770100
2.3669-2.44330.23521490.191426352784100
2.4433-2.53060.23521510.195626352786100
2.5306-2.63190.24071310.198626772808100
2.6319-2.75170.20951240.202226492773100
2.7517-2.89670.21261460.202126462792100
2.8967-3.07810.25941420.214926772819100
3.0781-3.31570.24261430.208926682811100
3.3157-3.64920.27681350.199526922827100
3.6492-4.17680.19781390.173226972836100
4.1768-5.26050.17661440.156427192863100
5.2605-40.64970.22911310.2012788291997

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