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

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Basic information

Entry
Database: PDB / ID: 7mwv
TitleStructure of the E. coli PutA proline dehydrogenase domain (residues 86-630) complexed with cyclopropanecarboxylic acid
ComponentsBifunctional protein PutA
KeywordsOXIDOREDUCTASE / BETA/ALPHA BARREL / FLAVOENZYME / PROLINE CATABOLISM
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / cyclopropanecarboxylic acid / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.69 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)62,7555
Polymers61,4511
Non-polymers1,3044
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.991, 141.738, 146.299
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-2108-

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, 251 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-ZPJ / cyclopropanecarboxylic acid


Mass: 86.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18-28% PEG 3000, 100 mM sodium citrate, soaked crystals with 50 mM cyclopropanecarboxylic acid
PH range: 5.6-6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.69→73.15 Å / Num. obs: 85319 / % possible obs: 99.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 30.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.045 / Rrim(I) all: 0.127 / Net I/σ(I): 15.2 / Num. measured all: 639699
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
1.69-1.727.12.9892936041120.21.173.2180.694.6
9.08-73.156.40.02740046210.9990.0110.02962.899.6

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Processing

Software
NameVersionClassification
PHENIX1.19.1refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3E2R

3e2r


Resolution: 1.69→73.15 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 26.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2405 4300 5.08 %
Rwork0.2127 80360 -
obs0.214 84660 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.46 Å2 / Biso mean: 39.9777 Å2 / Biso min: 19.73 Å2
Refinement stepCycle: final / Resolution: 1.69→73.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3724 0 88 247 4059
Biso mean--32.77 37.88 -
Num. residues----499
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 (%)
1.69-1.710.6534930.65772010210375
1.71-1.730.58111460.57762611275797
1.73-1.750.5661380.52672663280199
1.75-1.770.52111430.478126502793100
1.77-1.790.4171580.411326692827100
1.79-1.820.39731560.384126622818100
1.82-1.840.36671390.344326702809100
1.84-1.870.32021700.309326902860100
1.87-1.90.30591430.267326812824100
1.9-1.930.28431350.247426662801100
1.93-1.960.25851490.2326872836100
1.96-20.22871420.230426902832100
2-2.040.27041300.236927012831100
2.04-2.080.28541350.248626932828100
2.08-2.120.27231470.252626902837100
2.12-2.170.26671330.237626692802100
2.17-2.230.27611360.209326932829100
2.23-2.290.25551330.210227232856100
2.29-2.360.26641500.207827072857100
2.36-2.430.2381400.203327002840100
2.43-2.520.2271690.203126822851100
2.52-2.620.22911760.204526702846100
2.62-2.740.2641490.205526852834100
2.74-2.880.27131410.216727322873100
2.88-3.060.2931450.219927282873100
3.06-3.30.20531280.203127442872100
3.3-3.630.20651480.195427532901100
3.63-4.160.17251450.167327392884100
4.16-5.240.16361410.153827872928100
5.24-73.150.22491420.188829153057100
Refinement TLS params.Method: refined / Origin x: 4.9564 Å / Origin y: 49.4609 Å / Origin z: 49.6543 Å
111213212223313233
T0.2045 Å2-0.0101 Å20.0198 Å2-0.3358 Å2-0.0268 Å2--0.1827 Å2
L0.6028 °2-0.145 °2-0.0924 °2-0.7843 °20.06 °2--1.0507 °2
S0.0406 Å °0.1144 Å °-0.0092 Å °-0.1193 Å °0.0298 Å °-0.0203 Å °-0.0984 Å °0.0868 Å °-0.0511 Å °
Refinement TLS groupSelection details: (chain 'A' and peptide)

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