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- PDB-6bsn: Structure of proline utilization A (PutA) with proline bound in r... -

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Basic information

Entry
Database: PDB / ID: 6bsn
TitleStructure of proline utilization A (PutA) with proline bound in remote sites
ComponentsBifunctional protein PutA
KeywordsOXIDOREDUCTASE / FLAVOENZYME / ROSSMANN FOLD / ALDEHYDE DEHYDROGENASE / FLAVIN ADENINE DINUCLEOTIDE / NICOTINAMIDE ADENINE DINUCLEOTIDE / PROLINE CATABOLISM / SUBSTRATE CHANNELING / BIFUNCTIONAL ENZYME
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 / proline biosynthetic process / 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 / proline biosynthetic process / cytoplasmic side of plasma membrane / DNA-binding transcription factor activity / nucleotide binding / DNA binding / identical protein binding / cytoplasm
Similarity search - Function
TIM Barrel - #220 / 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 ...TIM Barrel - #220 / 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; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / 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 / TIM Barrel / Alpha-Beta Barrel / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / PROLINE / Bifunctional protein PutA
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsTanner, J.J. / Korasick, D.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM065546 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM061068 United States
CitationJournal: Molecules / Year: 2017
Title: Structural Basis for the Substrate Inhibition of Proline Utilization A by Proline.
Authors: Korasick, D.A. / Pemberton, T.A. / Arentson, B.W. / Becker, D.F. / Tanner, J.J.
History
DepositionDec 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional protein PutA
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,28827
Polymers215,3322
Non-polymers3,95625
Water12,953719
1
A: Bifunctional protein PutA
B: Bifunctional protein PutA
hetero molecules

A: Bifunctional protein PutA
B: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)438,57554
Polymers430,6634
Non-polymers7,91250
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area27600 Å2
ΔGint-474 kcal/mol
Surface area131620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.757, 194.210, 108.738
Angle α, β, γ (deg.)90.000, 121.390, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 123 or resid 131...
21(chain B and (resid 4 through 51 or resid 55...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 4 through 123 or resid 131...A4 - 123
121(chain A and (resid 4 through 123 or resid 131...A131 - 145
131(chain A and (resid 4 through 123 or resid 131...A147 - 182
141(chain A and (resid 4 through 123 or resid 131...A183 - 184
151(chain A and (resid 4 through 123 or resid 131...A1 - 2001
161(chain A and (resid 4 through 123 or resid 131...A1 - 2001
171(chain A and (resid 4 through 123 or resid 131...A1 - 2001
181(chain A and (resid 4 through 123 or resid 131...A1 - 2001
211(chain B and (resid 4 through 51 or resid 55...B4 - 51
221(chain B and (resid 4 through 51 or resid 55...B55 - 63
231(chain B and (resid 4 through 51 or resid 55...B64
241(chain B and (resid 4 through 51 or resid 55...B4 - 2002
251(chain B and (resid 4 through 51 or resid 55...B4 - 2002
261(chain B and (resid 4 through 51 or resid 55...B4 - 2002
271(chain B and (resid 4 through 51 or resid 55...B4 - 2002

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Components

#1: Protein Bifunctional protein PutA


Mass: 107665.781 Da / Num. of mol.: 2 / Mutation: C792A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110) (bacteria)
Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110 / Gene: putA / Production host: Escherichia coli (E. coli) / References: UniProt: Q89E26
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical
ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 719 / 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: 3.49 Å3/Da / Density % sol: 64.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 2 M ammonium sulfate and 0.1 M Tris / PH range: 7-8

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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: Dec 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→47.02 Å / Num. obs: 311518 / % possible obs: 99.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 31.31 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.054 / Rrim(I) all: 0.105 / Net I/σ(I): 8.7
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.787 / Num. unique obs: 7418 / CC1/2: 0.649 / Rpim(I) all: 0.563 / Rrim(I) all: 0.975 / % possible all: 94.1

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3haz

3haz


Resolution: 2.15→47.019 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.44
RfactorNum. reflection% reflection
Rfree0.239 15658 5.03 %
Rwork0.2086 --
obs0.2102 158149 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.63 Å2 / Biso mean: 39.6665 Å2 / Biso min: 17.98 Å2
Refinement stepCycle: final / Resolution: 2.15→47.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14521 0 240 719 15480
Biso mean--49.21 37.3 -
Num. residues----1947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715070
X-RAY DIFFRACTIONf_angle_d0.8920517
X-RAY DIFFRACTIONf_chiral_restr0.052351
X-RAY DIFFRACTIONf_plane_restr0.0062688
X-RAY DIFFRACTIONf_dihedral_angle_d19.9159095
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8849X-RAY DIFFRACTION5.656TORSIONAL
12B8849X-RAY DIFFRACTION5.656TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.17440.37894530.31978874932787
2.1744-2.20.32344520.31728785923788
2.2-2.22690.35754680.31399170963891
2.2269-2.2550.38085790.333696341021397
2.255-2.28470.29935060.2637100411054799
2.2847-2.3160.28855200.24711003910559100
2.316-2.34910.28684760.2498992510401100
2.3491-2.38420.28435070.24091003810545100
2.3842-2.42140.28986250.24511001610641100
2.4214-2.46110.3115740.2482998110555100
2.4611-2.50350.28564680.24451001010478100
2.5035-2.54910.25974730.22581006910542100
2.5491-2.59810.25174960.22611004110537100
2.5981-2.65110.27525280.24171006910597100
2.6511-2.70880.30155210.250198921041399
2.7088-2.77180.28665000.23291007810578100
2.7718-2.84110.275640.2295992710491100
2.8411-2.91790.24875610.221899871054899
2.9179-3.00370.28075110.226199021041399
3.0037-3.10070.275270.2378100241055199
3.1007-3.21140.25165560.222398921044899
3.2114-3.340.23945250.224699671049299
3.34-3.4920.22434950.203298821037799
3.492-3.6760.22155390.193699161045599
3.676-3.90620.20015530.174299191047299
3.9062-4.20760.20295200.165599401046099
4.2076-4.63070.18375890.154899281051799
4.6307-5.30.19025230.1699361045999
5.3-6.67440.21225230.184799831050699
6.6744-47.02990.18565260.181899951052199
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)
10.434-0.08360.10340.7501-0.24660.3312-0.0305-0.0606-0.03890.13380.05120.1251-0.07990.0458-0.02220.2343-0.00610.05080.24750.01570.18783.2862-7.9002-26.9688
20.44750.0918-0.08570.7752-0.24550.3493-0.03680.08980.1839-0.14110.06840.12910.07020.0735-0.02970.2410.0114-0.07460.29360.05580.31123.102143.6479-65.4979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and not resname FDAA0
2X-RAY DIFFRACTION2chain B and not resname FDAB0

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