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- PDB-7n4w: Complex structure of ROTU4 with rotundine -

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Basic information

Entry
Database: PDB / ID: 7n4w
TitleComplex structure of ROTU4 with rotundine
ComponentsROTU4
KeywordsTRANSCRIPTION / Transcription Factor / Protein Engineering / Specificity / Synthetic Biology
Function / homologyrotundine
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsKim, W. / Zhang, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104896 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM125882 United States
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Using fungible biosensors to evolve improved alkaloid biosyntheses.
Authors: d'Oelsnitz, S. / Kim, W. / Burkholder, N.T. / Javanmardi, K. / Thyer, R. / Zhang, Y. / Alper, H.S. / Ellington, A.D.
History
DepositionJun 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 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 1.2Sep 7, 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: ROTU4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6894
Polymers22,1451
Non-polymers5443
Water1,964109
1
A: ROTU4
hetero molecules

A: ROTU4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3788
Polymers44,2912
Non-polymers1,0876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3340 Å2
ΔGint-49 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.880, 50.610, 46.079
Angle α, β, γ (deg.)90.000, 90.120, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-336-

HOH

21A-405-

HOH

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Components

#1: Protein ROTU4


Mass: 22145.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-P4V / rotundine


Mass: 355.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25NO4 / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.2 M ammonium sulfate, 0.1 M sodium chloride, 0.1 M MES
PH range: 6.0 - 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.802
11-h,-k,l20.198
ReflectionResolution: 1.64→50 Å / Num. obs: 39481 / % possible obs: 96 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.056 / Rrim(I) all: 0.083 / Χ2: 1.373 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.73-1.761.80.28519990.830.2630.3890.54895.1
1.76-1.791.90.26319520.840.2410.3580.57795.1
1.79-1.8320.24319040.8550.2220.3310.61395.2
1.83-1.8620.20719970.8760.1910.2820.69895
1.86-1.91.90.1919820.8920.1750.2590.82495.6
1.9-1.951.90.16819650.9150.1540.2290.8195.5
1.95-21.90.15318930.920.1410.2081.14694.8
2-2.051.90.12419940.9440.1140.1691.03996.4
2.05-2.111.90.11519910.9530.1070.1581.23296
2.11-2.181.90.10619580.9530.0970.1441.32896.2
2.18-2.2620.09619440.9590.0890.1311.43895.9
2.26-2.3520.08920250.9650.0820.1211.6796.4
2.35-2.451.90.08519210.9650.0790.1161.73595.2
2.45-2.581.90.07719700.9670.0710.1051.8196.2
2.58-2.751.90.07119890.9730.0660.0981.91296
2.75-2.9620.06419960.9770.060.0881.87695.9
2.96-3.2620.06119720.9780.0560.0832.11296.4
3.26-3.731.90.05719490.9830.0530.0782.53397
3.73-4.6920.04820370.9860.0450.0662.29297.9
4.69-501.90.03520430.9940.0320.0481.17499.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VVX

3vvx


Resolution: 1.64→46.08 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.919 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.016 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1735 1364 5.5 %RANDOM
Rwork0.1509 ---
obs0.1522 23459 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.41 Å2 / Biso mean: 27.781 Å2 / Biso min: 15.5 Å2
Baniso -1Baniso -2Baniso -3
1--6.62 Å2-0 Å27.18 Å2
2--5.54 Å20 Å2
3---1.08 Å2
Refinement stepCycle: final / Resolution: 1.64→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1461 0 37 109 1607
Biso mean--24.99 38.71 -
Num. residues----183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121528
X-RAY DIFFRACTIONr_angle_refined_deg2.2461.662063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5695182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22720.58885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41615262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5411514
X-RAY DIFFRACTIONr_chiral_restr0.3190.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021155
LS refinement shellResolution: 1.64→1.681 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.267 100 -
Rwork0.181 1596 -
obs--93.39 %

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