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- PDB-6vz9: Structure of proline utilization A with the FAD covalently modifi... -

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Basic information

Entry
Database: PDB / ID: 6vz9
TitleStructure of proline utilization A with the FAD covalently modified by L-thiazolidine-2-carboxylate
ComponentsBifunctional protein PutA
KeywordsOXIDOREDUCTASE / FLAVOENZYME / ROSSMANN FOLD / 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 / : / cytoplasmic side of plasma membrane / DNA-binding transcription factor activity / nucleotide binding / DNA binding
Similarity search - Function
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 ...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 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / (2S)-1,3-thiazolidine-2-carboxylic acid / Bifunctional protein PutA
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.52 Å
AuthorsCampbell, A.C. / Tanner, J.J.
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: Acs Chem.Biol. / Year: 2020
Title: Covalent Modification of the Flavin in Proline Dehydrogenase by Thiazolidine-2-Carboxylate.
Authors: Campbell, A.C. / Becker, D.F. / Gates, K.S. / Tanner, J.J.
History
DepositionFeb 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 2, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Sep 9, 2020Group: Database references / Category: citation / citation_author
Revision 1.4Oct 11, 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)268,16120
Polymers263,9232
Non-polymers4,23818
Water42,6232366
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10950 Å2
ΔGint-166 kcal/mol
Surface area78790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.961, 102.104, 126.379
Angle α, β, γ (deg.)90.000, 106.350, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bifunctional protein PutA


Mass: 131961.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (strain SM11) (bacteria)
Strain: SM11 / Gene: putA, SM11_chr0102 / Production host: Escherichia coli (E. coli)
References: UniProt: F7X6I3, proline dehydrogenase, L-glutamate gamma-semialdehyde dehydrogenase

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Non-polymers , 8 types, 2384 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-T2C / (2S)-1,3-thiazolidine-2-carboxylic acid


Mass: 133.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO2S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2366 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG-3350, 0.2M AMMONIUM SULFATE, REMARK 280 0.1M MGCL2, 0.1M HEPES, 0.1M NA FORMATE, 10MM NAD+, 50MM thiazolidine-2-carboxylate, PH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Feb 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→48.44 Å / Num. obs: 708036 / % possible obs: 99.1 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.048 / Rrim(I) all: 0.091 / Net I/σ(I): 10.9 / Num. measured all: 1321174 / Scaling rejects: 302
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.377 / Num. measured all: 53582 / Num. unique obs: 17048 / CC1/2: 0.354 / Rpim(I) all: 0.916 / Rrim(I) all: 1.663 / Net I/σ(I) obs: 0.7 / % possible all: 91.5

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5KF6

5kf6


Resolution: 1.52→48.44 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.97 / Phase error: 22.26
RfactorNum. reflection% reflection
Rfree0.207 35301 4.99 %
Rwork0.18 672735 -
obs0.181 708036 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.19 Å2 / Biso mean: 24.44 Å2 / Biso min: 8.55 Å2
Refinement stepCycle: final / Resolution: 1.52→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18096 0 269 2366 20731
Biso mean--26.63 31.02 -
Num. residues----2434
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 (%)
1.52-1.53730.35229800.3386176581863875
1.5373-1.55540.345911370.3221208152195288
1.5554-1.57430.326511500.3125235152466599
1.5743-1.59430.322913230.3001232782460199
1.5943-1.61520.310111790.2948234532463299
1.6152-1.63740.311811780.2879233312450999
1.6374-1.66080.286712760.2758234472472399
1.6608-1.68560.293712250.2713233512457699
1.6856-1.71190.297612350.2654229862422197
1.7119-1.740.268811380.2535222262336494
1.74-1.770.274312350.2453220862332194
1.77-1.80220.258711700.2398221532332394
1.8022-1.83680.266211660.2352222452341194
1.8368-1.87430.244211610.2221219952315694
1.8743-1.91510.245610780.2151220712314993
1.9151-1.95960.239211940.2049221282332294
1.9596-2.00860.236411740.1942231752434998
2.0086-2.06290.236712170.192229622417997
2.0629-2.12360.20711710.1803231812435298
2.1236-2.19220.20112510.1683230292428098
2.1922-2.27050.204712330.1669226432387696
2.2705-2.36140.198312330.1645229652419897
2.3614-2.46890.206412050.1619229622416797
2.4689-2.59910.196211230.1646228492397296
2.5991-2.76190.196112180.1656224802369895
2.7619-2.97510.182411670.1608223032347095
2.9751-3.27440.182310870.1625220402312793
3.2744-3.74810.169510940.1474216172271191
3.7481-4.72160.140812020.122216052280792
4.7216-48.440.15911010.1335221862328794
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)
10.7301-0.02170.22790.0776-0.0410.1548-0.0436-0.11080.01370.02870.03630.019-0.0236-0.03760.00510.1430.02050.01560.10710.00090.1196-25.592465.448492.938
20.1901-0.00110.07860.2304-0.04440.39830.0161-0.035-0.00870.0460.00110.00350.0417-0.0865-0.01950.1006-0.00270.00290.1083-0.01060.1065.614530.83691.7888
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND PEPTIDEA14 - 1223
2X-RAY DIFFRACTION2CHAIN B AND PEPTIDEB14 - 1223

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