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- PDB-6nl2: Apo NIS synthetase DesD variant R306Q -

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Basic information

Entry
Database: PDB / ID: 6nl2
TitleApo NIS synthetase DesD variant R306Q
Componentsdesferrioxamine E biosynthesis protein DesD
KeywordsBIOSYNTHETIC PROTEIN / NIS synthetase / catalytic variant / siderophore synthesis
Function / homology
Function and homology information


acid-amino acid ligase activity / siderophore biosynthetic process
Similarity search - Function
Transferase(Phosphotransferase); domain 1 - #40 / TATA-Binding Protein - #280 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3370 / Aerobactin siderophore biosynthesis, IucA/IucC, N-terminal / Aerobactin siderophore biosynthesis, IucA/IucC-like / IucA / IucC family / Ferric iron reductase FhuF domain / Ferric iron reductase FhuF-like transporter / TATA-Binding Protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Transferase(Phosphotransferase); domain 1 - #40 / TATA-Binding Protein - #280 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3370 / Aerobactin siderophore biosynthesis, IucA/IucC, N-terminal / Aerobactin siderophore biosynthesis, IucA/IucC-like / IucA / IucC family / Ferric iron reductase FhuF domain / Ferric iron reductase FhuF-like transporter / TATA-Binding Protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Transferase(Phosphotransferase); domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsHoffmann, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1716986 United States
CitationJournal: To Be Published
Title: A C-terminal Loop Mediates Cooperativity in the NIS Synthetase DesD
Authors: Hoffmann, K.M. / Amendola, C. / Goncuian, E. / Karimi, K. / Kovak, J. / Mojab, Y. / Prussia, G.
History
DepositionJan 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Assembly

Deposited unit
A: desferrioxamine E biosynthesis protein DesD
B: desferrioxamine E biosynthesis protein DesD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,06916
Polymers132,9502
Non-polymers1,11914
Water13,277737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-73 kcal/mol
Surface area42500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.322, 95.696, 181.624
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein desferrioxamine E biosynthesis protein DesD


Mass: 66474.922 Da / Num. of mol.: 2 / Mutation: R306Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SCO2785 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L069
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 737 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.16 M magnesium chloride hexahydrate, 0.08 M Tris hydrochloride, pH 8.5, 24% w/v PEG4000, 20% v/v glycerol
Temp details: ambient room temperature

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Nov 30, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→60.54 Å / Num. obs: 98322 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 13.62 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.035 / Rrim(I) all: 0.096 / Χ2: 0.99 / Net I/σ(I): 15.8
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 7 / Num. unique obs: 4819 / CC1/2: 0.945 / Rpim(I) all: 0.093 / Rrim(I) all: 0.254 / Χ2: 0.84 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2X0O

2x0o


Resolution: 1.92→58.27 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1863 4796 4.9 %RANDOM
Rwork0.1595 ---
obs0.1608 93456 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.54 Å2 / Biso mean: 19.017 Å2 / Biso min: 8.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å2-0 Å2
2--1.62 Å2-0 Å2
3----1.22 Å2
Refinement stepCycle: final / Resolution: 1.92→58.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9370 0 69 737 10176
Biso mean--26.89 26.27 -
Num. residues----1187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0139697
X-RAY DIFFRACTIONr_bond_other_d0.0350.0178902
X-RAY DIFFRACTIONr_angle_refined_deg2.6481.64213192
X-RAY DIFFRACTIONr_angle_other_deg2.5681.5720530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26551199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.51521.059557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.729151521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3021586
X-RAY DIFFRACTIONr_chiral_restr0.1820.21220
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0210999
X-RAY DIFFRACTIONr_gen_planes_other0.0290.022201
X-RAY DIFFRACTIONr_mcbond_it1.3151.9254763
X-RAY DIFFRACTIONr_mcbond_other1.3141.9254761
X-RAY DIFFRACTIONr_mcangle_it2.1982.8825955
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 352 -
Rwork0.174 6802 -
all-7154 -
obs--99.76 %

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