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- PDB-6u1r: SxtG an amidinotransferase from the Microseira wollei in Saxitoxi... -

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Basic information

Entry
Database: PDB / ID: 6u1r
TitleSxtG an amidinotransferase from the Microseira wollei in Saxitoxin biosynthetic pathway
ComponentsSxtG
KeywordsTRANSFERASE / amidinotransferase / saxitoxin biosynthetic pathway / SxtG
Function / homologyamidinotransferase activity / Glycine/inosamine-phosphate amidinotransferase / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta / FORMIC ACID / SxtG
Function and homology information
Biological speciesMicroseira wollei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.792 Å
AuthorsMallik, L. / Lukowski, A.L. / Narayan, A.R.H. / Koutmos, M.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Substrate Promiscuity of a Paralytic Shellfish Toxin Amidinotransferase.
Authors: Lukowski, A.L. / Mallik, L. / Hinze, M.E. / Carlson, B.M. / Ellinwood, D.C. / Pyser, J.B. / Koutmos, M. / Narayan, A.R.H.
History
DepositionAug 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: 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 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SxtG
B: SxtG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8223
Polymers87,7762
Non-polymers461
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-15 kcal/mol
Surface area25870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.378, 100.562, 163.941
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein SxtG


Mass: 43887.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microseira wollei (bacteria) / Gene: sxtG / Plasmid: pET151 / Details (production host): T7 promoter and TEV cleavable / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: C3RVP0
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 3350, 0.2 M ammonium acetate and 0.1 M bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 13, 2018
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.79→48.1 Å / Num. obs: 77125 / % possible obs: 99.3 % / Redundancy: 7.2 % / Biso Wilson estimate: 29.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.033 / Rrim(I) all: 0.091 / Χ2: 0.087 / Net I/σ(I): 17.1
Reflection shellResolution: 1.79→1.83 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4162 / CC1/2: 0.871 / Rpim(I) all: 0.282 / Rrim(I) all: 0.733 / Χ2: 0.76 / % possible all: 90.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JDW

1jdw


Resolution: 1.792→48.071 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1948 3955 5.13 %
Rwork0.1671 --
obs0.1686 77058 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.792→48.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5669 0 3 592 6264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085887
X-RAY DIFFRACTIONf_angle_d0.9288021
X-RAY DIFFRACTIONf_dihedral_angle_d11.7913511
X-RAY DIFFRACTIONf_chiral_restr0.057850
X-RAY DIFFRACTIONf_plane_restr0.0061048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.792-1.81360.32871340.27542185X-RAY DIFFRACTION84
1.8136-1.83660.27291460.25672600X-RAY DIFFRACTION100
1.8366-1.86070.28671420.24182551X-RAY DIFFRACTION99
1.8607-1.88620.26261310.21492607X-RAY DIFFRACTION99
1.8862-1.91320.24831360.19992581X-RAY DIFFRACTION100
1.9132-1.94170.23261390.19352577X-RAY DIFFRACTION100
1.9417-1.97210.21761350.1922637X-RAY DIFFRACTION100
1.9721-2.00440.21971360.17572578X-RAY DIFFRACTION100
2.0044-2.0390.22511230.18092608X-RAY DIFFRACTION100
2.039-2.07610.21811290.18022606X-RAY DIFFRACTION100
2.0761-2.1160.20271230.16872608X-RAY DIFFRACTION100
2.116-2.15920.19821600.16362600X-RAY DIFFRACTION100
2.1592-2.20610.17591400.16422586X-RAY DIFFRACTION100
2.2061-2.25740.21741340.16432600X-RAY DIFFRACTION99
2.2574-2.31390.19861380.1622613X-RAY DIFFRACTION100
2.3139-2.37650.21911360.16532628X-RAY DIFFRACTION100
2.3765-2.44640.17271420.15822613X-RAY DIFFRACTION100
2.4464-2.52530.19321440.15862597X-RAY DIFFRACTION100
2.5253-2.61560.18671360.16042644X-RAY DIFFRACTION100
2.6156-2.72030.21421450.16222631X-RAY DIFFRACTION100
2.7203-2.84410.20451560.16932597X-RAY DIFFRACTION100
2.8441-2.9940.1931430.16832638X-RAY DIFFRACTION100
2.994-3.18160.18071500.16622644X-RAY DIFFRACTION100
3.1816-3.42720.21041520.1722665X-RAY DIFFRACTION100
3.4272-3.77190.17631540.15112659X-RAY DIFFRACTION100
3.7719-4.31740.17131320.14372700X-RAY DIFFRACTION100
4.3174-5.43830.13831480.1322727X-RAY DIFFRACTION100
5.4383-48.0710.18611710.1862823X-RAY DIFFRACTION99

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