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- PDB-7sqn: Structure of the E. coli PutA proline dehydrogenase domain (resid... -

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Basic information

Entry
Database: PDB / ID: 7sqn
TitleStructure of the E. coli PutA proline dehydrogenase domain (residues 86-630) complexed with (2S)-oxetane-2-carboxylic acid
ComponentsBifunctional protein PutA
KeywordsOXIDOREDUCTASE / BETA/ALPHA BARREL / FLAVOENZYME / PROLINE CATABOLISM
Function / homology(2S)-oxetane-2-carboxylic acid / FLAVIN-ADENINE DINUCLEOTIDE / TRIETHYLENE GLYCOL / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 Å
AuthorsTanner, J.J. / Bogner, A.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132640 United States
CitationJournal: Org.Biomol.Chem. / Year: 2022
Title: Structure-affinity relationships of reversible proline analog inhibitors targeting proline dehydrogenase.
Authors: Bogner, A.N. / Tanner, J.J.
History
DepositionNov 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional protein PutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7275
Polymers61,4511
Non-polymers1,2764
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.854, 140.984, 145.962
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2103-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bifunctional protein PutA


Mass: 61451.102 Da / Num. of mol.: 1 / Fragment: residues 86-630
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: putA, SAMEA3472047_03659 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A383H020, proline dehydrogenase, L-glutamate gamma-semialdehyde dehydrogenase

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Non-polymers , 5 types, 62 molecules

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


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-A8G / (2S)-oxetane-2-carboxylic acid


Mass: 102.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.81 Å3/Da / Density % sol: 56.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate pH 5.6, 5.75, 5.9 or 6.0 and 18-28% PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.25→64.72 Å / Num. obs: 35985 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 55.05 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.053 / Rrim(I) all: 0.126 / Net I/σ(I): 6.3 / Num. measured all: 191098 / Scaling rejects: 86
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
2.25-2.325.51.3151800932680.5950.61.451199.9
9-64.7250.08831116280.9870.0410.0981799.2

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.19.1refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7MWU

7mwu


Resolution: 2.25→64.72 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 1816 5.07 %
Rwork0.2081 33971 -
obs0.2099 35787 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.66 Å2 / Biso mean: 69.6152 Å2 / Biso min: 37.42 Å2
Refinement stepCycle: final / Resolution: 2.25→64.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3752 0 86 58 3896
Biso mean--56.61 52.11 -
Num. residues----503
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.310.35121540.33382543269799
2.31-2.380.35311400.31152566270699
2.38-2.460.3291160.28972574269098
2.46-2.540.32691270.31042578270599
2.54-2.650.36251300.26972600273099
2.65-2.770.30181590.23942588274799
2.77-2.910.24461290.23612607273699
2.91-3.090.27341230.24832586270999
3.09-3.330.26091400.237926262766100
3.33-3.670.25771600.211825952755100
3.67-4.20.21491480.187126432791100
4.2-5.290.1951670.161726632830100
5.29-64.720.21991230.1782802292599
Refinement TLS params.Method: refined / Origin x: 4.9795 Å / Origin y: 49.4039 Å / Origin z: 49.3375 Å
111213212223313233
T0.4039 Å2-0.036 Å20.0468 Å2-0.3881 Å2-0.04 Å2--0.3432 Å2
L0.895 °2-0.204 °2-0.0021 °2-1.3776 °2-0.0134 °2--2.2723 °2
S0.0551 Å °0.1291 Å °0.0034 Å °-0.2445 Å °0.0696 Å °-0.0589 Å °-0.1858 Å °0.2306 Å °-0.069 Å °
Refinement TLS groupSelection details: chain A and peptide

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