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- PDB-4q72: Crystal Structure of Bradyrhizobium japonicum Proline Utilization... -

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Basic information

Entry
Database: PDB / ID: 4q72
TitleCrystal Structure of Bradyrhizobium japonicum Proline Utilization A (PutA) Mutant D779Y
ComponentsProline dehydrogenase
KeywordsOXIDOREDUCTASE / PROLINE UTILIZATION A / PUTA / BETA-ALPHA BARREL / ROSSMANN FOLD / PROLINE DEHYDROGENASE / 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE / FAD Binding
Function / homology
Function and homology information


proline dehydrogenase / proline dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / L-glutamate gamma-semialdehyde dehydrogenase activity / L-proline catabolic process to L-glutamate / : / cytoplasmic side of plasma membrane / DNA-binding transcription factor activity / nucleotide binding / DNA binding ...proline dehydrogenase / proline dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / L-glutamate gamma-semialdehyde dehydrogenase activity / L-proline catabolic process to L-glutamate / : / cytoplasmic side of plasma membrane / DNA-binding transcription factor activity / nucleotide binding / DNA binding / identical protein binding / cytoplasm
Similarity search - Function
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 / Aldehyde dehydrogenase, cysteine active site ...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 / 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
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Bifunctional protein PutA
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsTanner, J.J. / Pemberton, T.A. / Luo, M.
CitationJournal: Biochemistry / Year: 2014
Title: Kinetic and Structural Characterization of Tunnel-Perturbing Mutants in Bradyrhizobium japonicum Proline Utilization A.
Authors: Arentson, B.W. / Luo, M. / Pemberton, T.A. / Tanner, J.J. / Becker, D.F.
History
DepositionApr 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
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

Downloads & links

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Assembly

Deposited unit
A: Proline dehydrogenase
B: Proline dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,91613
Polymers215,4922
Non-polymers2,42411
Water5,332296
1
A: Proline dehydrogenase
B: Proline dehydrogenase
hetero molecules

A: Proline dehydrogenase
B: Proline dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)435,83126
Polymers430,9844
Non-polymers4,84822
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area25050 Å2
ΔGint-268 kcal/mol
Surface area134000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.110, 195.990, 108.700
Angle α, β, γ (deg.)90.000, 121.440, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Proline dehydrogenase


Mass: 107745.930 Da / Num. of mol.: 2 / Mutation: D779Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium diazoefficiens (bacteria)
Strain: USDA 110 / Gene: BJ6T_21270, blr7261, putA / Plasmid: PKA8H / Production host: Escherichia coli (E. coli)
References: UniProt: Q89E26, EC: 1.5.99.8, L-glutamate gamma-semialdehyde dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIT APPEARS THAT B. JAPONICUM STRAIN USDA 110 HAS BEEN RECLASSIFIED AS BRADYRHIZOBIUM DIAZOEFFICIENS. ...IT APPEARS THAT B. JAPONICUM STRAIN USDA 110 HAS BEEN RECLASSIFIED AS BRADYRHIZOBIUM DIAZOEFFICIENS. SEE ALSO INT J SYST EVOL REMARK 999 MICROBIOL. 2013 SEP;63(PT 9):3342-51. DOI: 10.1099/IJS.0.049130-0.EPUB 2013 MAR 15. POLYPHASIC EVIDENCE SUPPORTING THE RECLASSIFICATION OF BRADYRHIZOBIUM JAPONICUM GROUP IA STRAINS AS BRADYRHIZOBIUM DIAZOEFFICIENS SP. NOV. PMID: 23504968

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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: 3.52 Å3/Da / Density % sol: 65.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.0 M AMMONIUM SULFATE, 0.1 M TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: May 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.088→115.296 Å / Num. all: 130815 / Num. obs: 130815 / % possible obs: 99.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 34.09 Å2 / Rsym value: 0.103 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.423.60.5151.469165189610.51598.8
2.42-2.573.70.3991.866247179770.39999
2.57-2.753.70.2832.562984169480.28399.1
2.75-2.973.70.1893.858982157740.18999.3
2.97-3.253.80.12654840145830.1299.5
3.25-3.643.80.0877.750080131990.08799.5
3.64-4.23.80.0718.944630116490.07199.7
4.2-5.143.90.0629.83816098830.06299.8
5.14-7.273.90.0698.62957076550.06999.9
7.27-31.9863.80.0726.51600041860.07298.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.21data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.14data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 3haz

3haz


Resolution: 2.3→31.986 Å / FOM work R set: 0.7765 / SU ML: 0.31 / σ(F): 1.35 / Phase error: 29.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 6542 5.03 %same test set as 3haz
Rwork0.2155 ---
obs0.2173 129985 98.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.25 Å2 / Biso mean: 38.81 Å2 / Biso min: 15.72 Å2
Refinement stepCycle: LAST / Resolution: 2.3→31.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14386 0 154 296 14836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814823
X-RAY DIFFRACTIONf_angle_d1.10720191
X-RAY DIFFRACTIONf_chiral_restr0.0642330
X-RAY DIFFRACTIONf_plane_restr0.0062646
X-RAY DIFFRACTIONf_dihedral_angle_d14.0635364
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 (%)
2.3-2.32610.36672200.27314087430798
2.3261-2.35350.3232090.27334058426798
2.3535-2.38220.32912380.25584113435198
2.3822-2.41230.33182010.26364088428998
2.4123-2.44410.31122350.26354020425598
2.4441-2.47750.39462250.26974094431998
2.4775-2.51290.33212130.27264076428998
2.5129-2.55040.30262190.2594076429598
2.5504-2.59020.35052010.25584112431398
2.5902-2.63270.29741820.25874109429198
2.6327-2.67810.30891980.26474095429398
2.6781-2.72670.30472080.25684100430898
2.7267-2.77910.30132320.24714091432398
2.7791-2.83580.29442290.24824071430099
2.8358-2.89750.28642290.24984085431498
2.8975-2.96480.30071960.24314111430799
2.9648-3.03890.32152090.24574144435399
3.0389-3.1210.29042280.23914140436899
3.121-3.21280.25542310.22634107433899
3.2128-3.31640.2642070.23234108431599
3.3164-3.43480.24852100.21874155436599
3.4348-3.57210.25232230.2164118434199
3.5721-3.73440.2532140.1974152436699
3.7344-3.9310.22172260.18474128435499
3.931-4.17680.20332170.17794147436499
4.1768-4.49850.19792310.16524130436199
4.4985-4.94970.18572540.1664142439699
4.9497-5.66250.2232270.185941474374100
5.6625-7.12110.2112170.209542124429100
7.1211-31.9890.19642130.20594227444099

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