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- PDB-5jgk: Crystal structure of GtmA in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 5jgk
TitleCrystal structure of GtmA in complex with SAH
ComponentsUbiE/COQ5 family methyltransferase, putative
KeywordsTRANSFERASE / Aspergillus fumigatus / Methyltransferase / S-ADENOSYL-L-HOMOCYSTEINE / Gliotoxin / Resistance
Function / homologyubiE/COQ5 methyltransferase family / S-adenosylmethionine-dependent methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / UbiE/COQ5 family methyltransferase, putative
Function and homology information
Biological speciesAspergillus fumigatus Z5 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsDolan, S.K. / Bock, T. / Hering, V. / Jones, G.W. / Blankenfeldt, W. / Dolye, S.
CitationJournal: Open Biol / Year: 2017
Title: Structural, mechanistic and functional insight into gliotoxinbis-thiomethylation inAspergillus fumigatus.
Authors: Dolan, S.K. / Bock, T. / Hering, V. / Owens, R.A. / Jones, G.W. / Blankenfeldt, W. / Doyle, S.
History
DepositionApr 20, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UbiE/COQ5 family methyltransferase, putative
B: UbiE/COQ5 family methyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1619
Polymers64,9122
Non-polymers1,2497
Water7,224401
1
A: UbiE/COQ5 family methyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0324
Polymers32,4561
Non-polymers5773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UbiE/COQ5 family methyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1295
Polymers32,4561
Non-polymers6734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.748, 109.301, 59.856
Angle α, β, γ (deg.)90.000, 112.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UbiE/COQ5 family methyltransferase, putative


Mass: 32455.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Z5 (mold) / Gene: Y699_02735 / Plasmid: pET19m / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J5Q3C4
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 2.4 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.33→45.12 Å / Num. obs: 130776 / % possible obs: 98.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 14.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.027 / Rrim(I) all: 0.07 / Net I/σ(I): 14.4 / Num. measured all: 852355 / Scaling rejects: 196
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.33-1.356.60.896199.1
7.28-45.126.70.04198.6

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→45.117 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.58
RfactorNum. reflection% reflection
Rfree0.1664 6485 4.96 %
Rwork0.1388 --
obs0.1401 130726 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.31 Å2 / Biso mean: 22.3843 Å2 / Biso min: 9.06 Å2
Refinement stepCycle: final / Resolution: 1.33→45.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4372 0 115 401 4888
Biso mean--22.17 29.92 -
Num. residues----562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074651
X-RAY DIFFRACTIONf_angle_d1.0246381
X-RAY DIFFRACTIONf_chiral_restr0.077726
X-RAY DIFFRACTIONf_plane_restr0.007815
X-RAY DIFFRACTIONf_dihedral_angle_d18.7081683
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.33-1.34510.24572190.20014085430499
1.3451-1.36090.21982490.19524163441299
1.3609-1.37750.24462230.18814083430699
1.3775-1.3950.22212320.17714204443699
1.395-1.41330.22772210.16444096431799
1.4133-1.43270.21732260.16024159438599
1.4327-1.45320.20961920.15084121431398
1.4532-1.47490.17812060.1444077428397
1.4749-1.49790.17422180.13254188440699
1.4979-1.52250.1482230.11784170439399
1.5225-1.54870.14471940.11024130432499
1.5487-1.57690.1632340.11554238447299
1.5769-1.60720.16452120.1144105431799
1.6072-1.640.14952150.11244137435299
1.64-1.67570.15372200.114149436999
1.6757-1.71470.14611980.11354137433598
1.7147-1.75750.15192200.11934103432398
1.7575-1.80510.18712300.11914180441099
1.8051-1.85820.15552110.11894157436899
1.8582-1.91820.15812250.12164165439099
1.9182-1.98670.17312210.1244147436899
1.9867-2.06630.17312090.12914162437199
2.0663-2.16030.16312120.13024104431698
2.1603-2.27420.15182000.12734102430297
2.2742-2.41670.16381810.13164200438199
2.4167-2.60330.1592180.14024199441799
2.6033-2.86520.17262190.154140435999
2.8652-3.27970.1741960.15994020421695
3.2797-4.13160.16642280.14494169439799
4.1316-45.14290.15042330.15044151438497

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