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- PDB-7n54: Complex structure of GLAU4 with glaucine -

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Basic information

Entry
Database: PDB / ID: 7n54
TitleComplex structure of GLAU4 with glaucine
ComponentsGLAU4
KeywordsTRANSCRIPTION / Transcription Factor / Protein Engineering / Specificity / Synthetic Biology
Function / homologyglaucine
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: GLAU4
B: GLAU4
C: GLAU4
D: GLAU4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,91412
Polymers88,1084
Non-polymers1,8068
Water6,017334
1
A: GLAU4
B: GLAU4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9576
Polymers44,0542
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-49 kcal/mol
Surface area17070 Å2
MethodPISA
2
C: GLAU4
D: GLAU4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9576
Polymers44,0542
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-49 kcal/mol
Surface area17140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.180, 54.198, 91.522
Angle α, β, γ (deg.)104.900, 98.000, 89.990
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
GLAU4


Mass: 22027.107 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-08V / glaucine / (6aS,11aM)-1,2,9,10-tetramethoxy-6-methyl-5,6,6a,7-tetrahydro-4H-dibenzo[de,g]quinoline


Mass: 355.428 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H25NO4 / Feature type: SUBJECT OF INVESTIGATION
Comment: antiinflammatory, channel blocker, inhibitor, alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
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

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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 PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 50154 / % possible obs: 94.3 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.056 / Rrim(I) all: 0.083 / Χ2: 1.062 / Net I/σ(I): 6.7 / Num. measured all: 90722
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.031.50.3222700.8130.30.440.52284.2
2.03-2.071.60.28323030.8210.2680.390.57387.6
2.07-2.111.70.24224450.8580.2270.3320.59291.7
2.11-2.151.90.21124630.9040.1960.2890.60491.1
2.15-2.21.80.18523920.9170.1750.2550.6393.5
2.2-2.251.80.1725280.930.1580.2320.71492.9
2.25-2.311.80.14625180.9390.1370.2010.79994.9
2.31-2.371.80.12725170.9560.1190.1750.89194.1
2.37-2.441.80.12525180.9530.1160.1710.92595.9
2.44-2.521.80.11225450.960.1040.1530.97895
2.52-2.611.90.125270.9670.0940.1381.03596
2.61-2.711.90.09225520.9710.0860.1261.00395.5
2.71-2.841.80.08125560.9780.0760.1111.09195.4
2.84-2.991.90.07225750.980.0670.0991.24997.1
2.99-3.171.90.06925700.980.0630.0941.39496.2
3.17-3.421.90.06125580.9840.0560.0831.45496.9
3.42-3.761.80.05625580.9880.0520.0771.58396.5
3.76-4.311.90.05226040.9880.0470.071.71496.6
4.31-5.431.90.0525730.9880.0460.0681.52497.1
5.43-501.90.04425820.9930.0410.061.34397.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18rc3_3805refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3VW0

3vw0


Resolution: 2→43.76 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 2.02 / Phase error: 25.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2323 2005 4 %
Rwork0.1989 48135 -
obs0.2003 50140 93.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.11 Å2 / Biso mean: 40.7541 Å2 / Biso min: 17.28 Å2
Refinement stepCycle: final / Resolution: 2→43.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5861 0 124 334 6319
Biso mean--31.84 43.75 -
Num. residues----735
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.28091270.25932910303780
2.05-2.110.2991370.24283266340390
2.11-2.170.29421360.23043447358392
2.17-2.240.271430.22933373351694
2.24-2.320.22781420.21783448359094
2.32-2.410.2731460.21173483362995
2.41-2.520.27231490.22033476362595
2.52-2.660.28261430.21853516365996
2.66-2.820.23841460.21053467361395
2.82-3.040.22971500.21053570372097
3.04-3.350.24131420.20173550369296
3.35-3.830.21131510.18363535368697
3.83-4.820.18881430.17283551369497
4.82-43.760.22761500.18933543369397

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