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

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Basic information

Entry
Database: PDB / ID: 7mwt
TitleStructure of the E. coli PutA proline dehydrogenase domain (residues 86-630) complexed with 1,1-Cyclobutanedicarboxylate
ComponentsBifunctional protein PutA
KeywordsOXIDOREDUCTASE / BETA/ALPHA BARREL / FLAVOENZYME / PROLINE CATABOLISM
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / TRIETHYLENE GLYCOL / cyclobutane-1,1-dicarboxylic acid / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.19 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
DepositionMay 17, 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)62,8216
Polymers61,4511
Non-polymers1,3705
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.803, 141.565, 144.974
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 , 6 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-ZPS / cyclobutane-1,1-dicarboxylic acid


Mass: 144.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 20-26% PEG 3350, 50-175 mM sodium citrate, soaked crystals with 50 mM cyclobutane-1,1-dicarboxylic acid

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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: Aug 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.19→101.26 Å / Num. obs: 38519 / % possible obs: 99.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 53.37 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.063 / Rrim(I) all: 0.139 / Net I/σ(I): 10.3 / Num. measured all: 183109
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
2.19-2.314.82.3442644455420.2341.2472.764199.7
6.93-101.264.50.038599513350.9980.0210.04737.199.2

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Processing

Software
NameVersionClassification
Aimless3.3.22data scaling
PHENIX1.14-3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3E2R

3e2r


Resolution: 2.19→70.78 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 31.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2574 1840 4.84 %
Rwork0.2234 36214 -
obs0.2251 38054 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.33 Å2 / Biso mean: 68.6201 Å2 / Biso min: 37.86 Å2
Refinement stepCycle: final / Resolution: 2.19→70.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3700 0 91 57 3848
Biso mean--57.82 50.65 -
Num. residues----499
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 (%)
2.19-2.250.40391420.38592497263989
2.25-2.320.36931490.35992635278495
2.32-2.390.361210.34572782290398
2.39-2.480.33131440.33562715285998
2.48-2.580.36891350.30472825296099
2.58-2.690.33361580.27482790294899
2.69-2.840.30731290.253628302959100
2.84-3.010.31941500.27172798294899
3.01-3.250.27561490.238228342983100
3.25-3.570.29811080.22822859296799
3.57-4.090.25181310.20032863299499
4.09-5.150.22151670.16692805297298
5.15-70.780.19411570.19492981313899
Refinement TLS params.Method: refined / Origin x: 4.9401 Å / Origin y: 49.9337 Å / Origin z: 49.1351 Å
111213212223313233
T0.58 Å2-0.0186 Å20.035 Å2-0.5524 Å2-0.0581 Å2--0.5591 Å2
L0.8922 °2-0.2 °20.0436 °2-1.1636 °2-0.2863 °2--2.1261 °2
S0.0576 Å °0.1329 Å °-0.0292 Å °-0.2689 Å °0.0792 Å °-0.0042 Å °-0.1248 Å °0.1849 Å °0.0023 Å °
Refinement TLS groupSelection details: peptide and chain A

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