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- PDB-3haz: Crystal structure of bifunctional proline utilization A (PutA) protein -

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Basic information

Entry
Database: PDB / ID: 3haz
TitleCrystal structure of bifunctional proline utilization A (PutA) protein
ComponentsProline dehydrogenase
KeywordsOXIDOREDUCTASE / Proline utilization A / PutA / flavoenzyme / proline dehydrogenase / 1-pyrroline-5-carboxylate 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 / cytoplasmic side of plasma membrane / DNA-binding transcription factor activity / nucleotide binding / DNA binding / identical protein binding
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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Bifunctional protein PutA
Similarity search - Component
Biological speciesBradyrhizobium japonicum USDA 110 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / combination of Se-Met MAD/SAD, molecular replacement / Resolution: 2.1 Å
AuthorsTanner, J.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Crystal structure of the bifunctional proline utilization A flavoenzyme from Bradyrhizobium japonicum
Authors: Srivastava, D. / Schuermann, J.P. / White, T.A. / Krishnan, N. / Sanyal, N. / Hura, G.L. / Tan, A. / Henzl, M.T. / Becker, D.F. / Tanner, J.J.
History
DepositionMay 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)220,09525
Polymers215,3962
Non-polymers4,69923
Water14,322795
1
A: Proline dehydrogenase
B: Proline dehydrogenase
hetero molecules

A: Proline dehydrogenase
B: Proline dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)440,19050
Polymers430,7914
Non-polymers9,39946
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area16850 Å2
ΔGint-61.6 kcal/mol
Surface area138210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.763, 195.846, 108.680
Angle α, β, γ (deg.)90.000, 121.480, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Proline dehydrogenase / Proline utilization A (PutA) bifunctional proline dehydrogenase and 1-pyrroline-5-carboxylate dehydrogenase


Mass: 107697.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Gly-His at the N-terminus is a cloning artifact.
Source: (gene. exp.) Bradyrhizobium japonicum USDA 110 (bacteria)
Gene: blr7261, putA / Plasmid: pKA8H / Production host: Escherichia coli (E. coli) / References: UniProt: Q89E26, EC: 1.5.99.8, EC: 1.5.1.12

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Non-polymers , 5 types, 818 molecules

#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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 795 / 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: 3.51 Å3/Da / Density % sol: 64.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2M Ammonium sulfate, 0.1 M Tris-HCl pH 7.0. N-terminal His tag cleaved by TEV protease, which leaves Gly-His at N-terminus., 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 2, 2007
RadiationMonochromator: beamline optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→43.27 Å / Num. obs: 172549 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 5.386
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.213.70.4121.893890251880.412100
2.21-2.353.80.3132.189339237800.313100
2.35-2.513.80.2393.184702224100.239100
2.51-2.713.80.1824.179097208150.182100
2.71-2.973.80.1315.673120191400.131100
2.97-3.323.80.0967.466528173710.096100
3.32-3.833.80.0728.958632153040.072100
3.83-4.73.80.0659.249733129650.065100
4.7-6.643.80.0649.438421100300.064100
6.64-43.273.70.077.22064155460.0799.6

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data processing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RESOLVEphasing
MOLREPphasing
RefinementMethod to determine structure: combination of Se-Met MAD/SAD, molecular replacement
Starting model: Partial model from MAD/SAD phasing from another crystal form

Resolution: 2.1→42.33 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.851 / SU ML: 0.67 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.233 8703 5.04 %random
Rwork0.2 ---
obs0.202 172521 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.55 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso max: 139.67 Å2 / Biso mean: 34.881 Å2 / Biso min: 9.46 Å2
Baniso -1Baniso -2Baniso -3
1--4.136 Å2-0 Å2-0.515 Å2
2---6.108 Å2-0 Å2
3---6.963 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14647 0 295 795 15737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515229
X-RAY DIFFRACTIONf_angle_d0.8620737
X-RAY DIFFRACTIONf_chiral_restr0.0522327
X-RAY DIFFRACTIONf_plane_restr0.0042703
X-RAY DIFFRACTIONf_dihedral_angle_d17.2575580
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.1240.2872670.24954785745
2.124-2.1490.2862720.23555045776
2.149-2.1750.2752950.23354285723
2.175-2.2030.2773240.22453525676
2.203-2.2320.272920.21454375729
2.232-2.2620.2622970.20855235820
2.262-2.2950.2313050.19954005705
2.295-2.3290.2562890.20554645753
2.329-2.3650.2482710.19854395710
2.365-2.4040.2522980.20554605758
2.404-2.4450.2783010.20754075708
2.445-2.490.2762850.2154855770
2.49-2.5380.2243010.19254315732
2.538-2.5890.2512720.254805752
2.589-2.6460.2412440.20954975741
2.646-2.7070.2622880.20854505738
2.707-2.7750.2432970.20354425739
2.775-2.850.2433110.20254185729
2.85-2.9340.2482740.20855225796
2.934-3.0290.2612720.21954545726
3.029-3.1370.2582950.21354695764
3.137-3.2620.2313030.20654095712
3.262-3.4110.2312690.19755075776
3.411-3.590.2152970.19354625759
3.59-3.8150.2412940.18354575751
3.815-4.1090.1922850.17254605745
4.109-4.5230.1923060.16354845790
4.523-5.1760.1833280.16554495777
5.176-6.5170.212880.19854935781
6.517-42.330.2012830.19955575840
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)
10.4295-0.12970.06560.8456-0.22650.1411-0.0425-0.0572-0.02820.17430.04240.1979-0.08620.0256-0.01560.09420.00510.06980.06670.02060.06213.3717-7.89-26.9285
20.51550.1137-0.05590.7245-0.22060.1847-0.04090.1110.2182-0.11750.07520.20650.08150.0426-0.02640.0773-0.0066-0.09480.0950.07890.17383.383244.0343-65.6021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 989
2X-RAY DIFFRACTION2chain BB2 - 989

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