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- PDB-5ux5: Structure of Proline Utilization A (PutA) from Corynebacterium fr... -

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Basic information

Entry
Database: PDB / ID: 5ux5
TitleStructure of Proline Utilization A (PutA) from Corynebacterium freiburgense
ComponentsBIFUNCTIONAL PROTEIN Proline utilization A (PutA)
KeywordsOXIDOREDUCTASE/TRANSFERASE / FLAVOENZYME / ROSSMANN FOLD / ALDEHYDE DEHYDROGENASE / PROLINE CATABOLISM / SUBSTRATE CHANNELING / BIFUNCTIONAL ENZYME / OXIDOREDUCTASE / OXIDOREDUCTASE-TRANSFERASE complex
Function / homology
Function and homology information


: / proline dehydrogenase activity / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / DNA-binding transcription factor activity / nucleotide binding
Similarity search - Function
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, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / BIFUNCTIONAL PROTEIN Proline utilization A (PutA)
Similarity search - Component
Biological speciesCorynebacterium freiburgense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTanner, J.J.
Funding support United States, 4items
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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM103335 United States
National Science Foundation (NSF, United States)DBI-1156692 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structure and characterization of a class 3B proline utilization A: Ligand-induced dimerization and importance of the C-terminal domain for catalysis.
Authors: Korasick, D.A. / Gamage, T.T. / Christgen, S. / Stiers, K.M. / Beamer, L.J. / Henzl, M.T. / Becker, D.F. / Tanner, J.J.
History
DepositionFeb 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Jun 21, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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 Proline utilization A (PutA)
B: BIFUNCTIONAL PROTEIN Proline utilization A (PutA)
C: BIFUNCTIONAL PROTEIN Proline utilization A (PutA)
D: BIFUNCTIONAL PROTEIN Proline utilization A (PutA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)483,72916
Polymers477,5484
Non-polymers6,18012
Water00
1
A: BIFUNCTIONAL PROTEIN Proline utilization A (PutA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,9324
Polymers119,3871
Non-polymers1,5453
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BIFUNCTIONAL PROTEIN Proline utilization A (PutA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,9324
Polymers119,3871
Non-polymers1,5453
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BIFUNCTIONAL PROTEIN Proline utilization A (PutA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,9324
Polymers119,3871
Non-polymers1,5453
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: BIFUNCTIONAL PROTEIN Proline utilization A (PutA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,9324
Polymers119,3871
Non-polymers1,5453
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.959, 116.360, 140.734
Angle α, β, γ (deg.)71.480, 89.680, 83.420
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 9 and (name N or name...
21(chain B and ((resid 9 and (name N or name...
31(chain C and ((resid 9 and (name N or name...
41(chain D and ((resid 9 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 9 and (name N or name...A0
211(chain B and ((resid 9 and (name N or name...B0
311(chain C and ((resid 9 and (name N or name...C0
411(chain D and ((resid 9 and (name N or name...D0

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Components

#1: Protein
BIFUNCTIONAL PROTEIN Proline utilization A (PutA)


Mass: 119387.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium freiburgense (bacteria)
Production host: Escherichia coli (E. coli)
References: UniProt: A0A1X8XLF1*PLUS, EC: 1.5.5.22, L-glutamate gamma-semialdehyde dehydrogenase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

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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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: The reservoir contained three volumes of solution A and one volume of solution B. Solution A:0.2 M magnesium chloride hexahydrate, 0.1 M Bis-tris pH 6.5, 25% w/v polyethylene glycol 3,350 ...Details: The reservoir contained three volumes of solution A and one volume of solution B. Solution A:0.2 M magnesium chloride hexahydrate, 0.1 M Bis-tris pH 6.5, 25% w/v polyethylene glycol 3,350 Solution B: 0.1 M HEPES pH 7.5, 10% w/v polyethylene glycol 6,000, 5% v/v (+/-)-2-Methyl-2, 4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→63.295 Å / Num. obs: 137220 / % possible obs: 98.5 % / Redundancy: 1.9 % / Biso Wilson estimate: 46.26 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.058 / Rrim(I) all: 0.082 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.7-2.751.90.4880.620.4850.68998
14.79-63.2920.0160.9990.0160.02397.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.9data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QAN

3qan


Resolution: 2.7→63.29 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.7
RfactorNum. reflection% reflection
Rfree0.2359 6784 4.95 %
Rwork0.1828 --
obs0.1854 137069 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.43 Å2 / Biso mean: 51.5769 Å2 / Biso min: 18.92 Å2
Refinement stepCycle: final / Resolution: 2.7→63.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29280 0 372 0 29652
Biso mean--58.6 --
Num. residues----3849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00930289
X-RAY DIFFRACTIONf_angle_d1.02941339
X-RAY DIFFRACTIONf_chiral_restr0.0554716
X-RAY DIFFRACTIONf_plane_restr0.0075365
X-RAY DIFFRACTIONf_dihedral_angle_d17.92718101
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A15628X-RAY DIFFRACTION6.906TORSIONAL
12B15628X-RAY DIFFRACTION6.906TORSIONAL
13C15628X-RAY DIFFRACTION6.906TORSIONAL
14D15628X-RAY DIFFRACTION6.906TORSIONAL
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 (%)
2.7-2.73070.34922210.27284316453798
2.7307-2.76280.33242370.27044320455798
2.7628-2.79650.31722500.25284245449598
2.7965-2.83190.3412370.25714383462098
2.8319-2.86920.33112300.26584255448598
2.8692-2.90850.33932230.26774353457698
2.9085-2.950.35831970.25864328452598
2.95-2.99410.30852220.25814336455898
2.9941-3.04080.31872140.24044336455098
3.0408-3.09070.29682600.23844264452498
3.0907-3.1440.31512210.24234382460398
3.144-3.20120.32472160.23454259447598
3.2012-3.26270.27982420.21814340458298
3.2627-3.32930.26862040.2264336454098
3.3293-3.40170.25992350.22154365460098
3.4017-3.48080.2512080.19834329453798
3.4808-3.56790.26032310.18154334456598
3.5679-3.66430.24552180.16814383460199
3.6643-3.77210.23882330.17144316454999
3.7721-3.89390.21072380.16334399463799
3.8939-4.0330.1932400.15734322456299
4.033-4.19450.18212040.14294384458899
4.1945-4.38530.18752380.13734355459399
4.3853-4.61650.18482220.13554359458199
4.6165-4.90560.18282290.13324374460399
4.9056-5.28420.19542020.15124431463399
5.2842-5.81560.22012250.16924380460599
5.8156-6.65640.21252090.16784377458699
6.6564-8.38330.19542240.15614399462399
8.3833-63.31190.17932560.15564323457999
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)
11.5455-0.17290.98180.4374-0.26021.1476-0.04690.23680.1957-0.0319-0.0392-0.0479-0.0230.0140.05550.3058-0.01370.05740.26510.04860.217986.2743108.1712-7.1082
21.5502-0.2696-0.37850.74370.16370.6539-0.04540.2605-0.4233-0.00170.06720.00750.17990.0579-0.02520.4256-0.0121-0.02210.2608-0.13680.3962108.077350.40639.2947
31.78520.19430.450.82370.13990.8379-0.0906-0.29990.50510.05430.08940.0218-0.1520.0611-0.00260.35090.02830.00860.3139-0.09970.445565.7702124.949452.4992
41.8704-0.1129-0.53260.4854-0.16490.9076-0.0906-0.4624-0.2385-0.02460.05570.0680.0736-0.06150.02290.32150.0121-0.03550.43940.13350.313643.953667.12568.7449
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and not (resname FAD or resname NAD)A0
2X-RAY DIFFRACTION2chain B and not (resname FAD or resname NAD)B0
3X-RAY DIFFRACTION3chain C and not (resname FAD or resname NAD)C0
4X-RAY DIFFRACTION4chain D and not (resname FAD or resname NAD)D0

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