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

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Basic information

Entry
Database: PDB / ID: 6ufp
TitleStructure of proline utilization A with the FAD covalently modified by L-thiazolidine-2-carboxylate and three cysteines (Cys46, Cys470, Cys638) modified to S,S-(2-HYDROXYETHYL)THIOCYSTEINE
Components(Bifunctional protein ...) x 2
KeywordsOXIDOREDUCTASE / FLAVOENZYME / ROSSMANN FOLD / PROLINE CATABOLISM / SUBSTRATE CHANNELING / BIFUNCTIONAL ENZYME
Function / homology
Function and homology information


proline dehydrogenase / proline dehydrogenase activity / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / L-glutamate gamma-semialdehyde dehydrogenase / proline biosynthetic process / 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, 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
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / FORMIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / (2S)-1,3-thiazolidine-2-carboxylic acid / Bifunctional protein PutA
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.737 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)R01GM061068 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM065546 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
DepositionSep 24, 2019Deposition 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 1.2Oct 11, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id

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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)268,35318
Polymers264,3042
Non-polymers4,04916
Water21,9601219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, see PDB 5KF6
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10440 Å2
ΔGint-123 kcal/mol
Surface area79950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.424, 102.108, 126.690
Angle α, β, γ (deg.)90.000, 106.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Bifunctional protein ... , 2 types, 2 molecules AB

#1: Protein Bifunctional protein PutA /


Mass: 132113.891 Da / Num. of mol.: 1
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
#2: Protein Bifunctional protein PutA /


Mass: 132190.000 Da / Num. of mol.: 1
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 , 7 types, 1235 molecules

#3: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1219 / 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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG-3350, 0.2M ammonium sulfate, 0.1M MgCl2, 0.1M HEPES, 0.1M Na formate, 10mM NAD+, 50mM T2C

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.737→121.5 Å / Num. obs: 251763 / % possible obs: 98.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 31.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.025 / Rrim(I) all: 0.049 / Net I/σ(I): 15.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.74-1.773.51.21640513115590.4410.7421.431192.3
9.51-121.53.90.02617415960.9990.0110.02355.197.2

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Processing

Software
NameVersionClassification
PHENIXdev_3120refinement
Aimless0.7.2data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5KF6

5kf6


Resolution: 1.737→121.495 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1998 12306 4.89 %
Rwork0.1677 239367 -
obs0.1693 251673 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.63 Å2 / Biso mean: 40.5359 Å2 / Biso min: 19.75 Å2
Refinement stepCycle: final / Resolution: 1.737→121.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17656 0 251 1219 19126
Biso mean--47.06 42.07 -
Num. residues----2394
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.737-1.75660.34853760.3108711089
1.7566-1.77720.33953850.3011799399
1.7772-1.79890.31114080.2857788198
1.7989-1.82170.29994220.26158039100
1.8217-1.84570.28454240.2388069100
1.8457-1.8710.28143890.248003100
1.871-1.89770.2764630.24077995100
1.8977-1.9260.31093920.2472803099
1.926-1.95610.26594140.22498007100
1.9561-1.98820.23093930.20428064100
1.9882-2.02250.24494280.19578005100
2.0225-2.05930.23864370.19638041100
2.0593-2.09890.23854170.1985789599
2.0989-2.14170.24474070.193799599
2.1417-2.18830.21744020.1855790098
2.1883-2.23920.23563880.18188069100
2.2392-2.29520.23234050.1827801299
2.2952-2.35730.21474010.17998109100
2.3573-2.42660.2384300.18218013100
2.4266-2.5050.22524390.17888015100
2.505-2.59450.21813880.18028062100
2.5945-2.69840.21323980.1772802399
2.6984-2.82120.21824180.1809795898
2.8212-2.96990.2134090.188015100
2.9699-3.1560.20144340.1786802599
3.156-3.39970.19394000.1698803599
3.3997-3.74190.18563890.153797798
3.7419-4.28340.15293970.1281793997
4.2834-5.39660.14534230.1214801898
5.3966-121.4950.15954300.1409807098
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)
10.86570.00980.30470.24240.02770.3743-0.0392-0.0446-0.00760.05360.04880.0008-0.0121-0.0066-0.00920.26090.01180.02020.19940.01480.226-25.807966.221893.5077
20.2496-0.03520.11910.4771-0.08060.60380.0188-0.04190.00020.10310.0352-0.00440.0635-0.0839-0.05520.19020.0068-0.00630.2258-0.01570.20435.868331.311691.4244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 14 through 1231)A14 - 1231
2X-RAY DIFFRACTION2(chain 'B' and resid 14 through 1231)B14 - 1231

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