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- PDB-6ea3: Thermobifida fusca FscH adenylation domain complexed with MbtH-li... -

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Basic information

Entry
Database: PDB / ID: 6ea3
TitleThermobifida fusca FscH adenylation domain complexed with MbtH-like protein FscK and Ser-AMP
Components
  • MbtH-like protein
  • adenylation domain of Fuscachelin synthetase component H
KeywordsLIGASE / siderophore biosynthesis / serine activating adenylation domain / MbtH-like protein / seryl-adenylate
Function / homology
Function and homology information


siderophore biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / lipid biosynthetic process / catalytic activity / phosphopantetheine binding / cytosol
Similarity search - Function
Rubredoxin-like / Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id / MbtH-like protein / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / ANL, N-terminal domain / Condensation domain / Condensation domain ...Rubredoxin-like / Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id / MbtH-like protein / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / ANL, N-terminal domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SERYL ADENYLATE / Amino acid adenylation / Putative conserved protein MbtH
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBruner, S.D. / Zagulyaeva, A.A.
CitationJournal: To Be Published
Title: Comprehensive analysis of protein-protein interactions between MbtH-like protein FscK and adenylation domains in nonribosomal biosynthesis of Fuscachelins.
Authors: Bruner, S.D. / Zagulyaeva, A.A.
History
DepositionAug 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: 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: MbtH-like protein
B: adenylation domain of Fuscachelin synthetase component H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7713
Polymers68,3362
Non-polymers4341
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-18 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.450, 68.760, 86.350
Angle α, β, γ (deg.)90.000, 104.810, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1297-

HOH

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Components

#1: Protein MbtH-like protein


Mass: 9094.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (strain YX) (bacteria)
Strain: YX / Gene: Tfu_1863 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q47NS3
#2: Protein adenylation domain of Fuscachelin synthetase component H


Mass: 59241.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (strain YX) (bacteria)
Strain: YX / Gene: Tfu_1866 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q47NS0
#3: Chemical ChemComp-SRP / SERYL ADENYLATE


Mass: 434.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N6O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 8000, sodium chloride, BisTris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 16, 2015
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.65→27.827 Å / Num. obs: 143171 / % possible obs: 96.8 % / Redundancy: 3.181 % / Biso Wilson estimate: 17.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.056 / Χ2: 1.03 / Net I/σ(I): 14.37 / Num. measured all: 455412 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.753.050.3432.89223500.8680.41893.2
1.75-1.93.0950.2074.8257640.9470.25195.1
1.9-2.13.1620.118.9241430.9850.13396.1
2.1-2.53.2090.06515.35286240.9940.07898
2.5-33.2640.04422.9177400.9970.05399
3-43.2790.03130.72142000.9980.03899.9
4-63.3560.02735.5873050.9980.03299.7
6-103.4770.02637.1724190.9990.03199.7
10-27.8273.110.02237.216260.9990.02794.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GR4

4gr4


Resolution: 1.65→27.827 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.49
RfactorNum. reflection% reflection
Rfree0.1864 2000 2.7 %
Rwork0.1649 --
obs0.1655 73978 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.2 Å2 / Biso mean: 23.0606 Å2 / Biso min: 10.19 Å2
Refinement stepCycle: final / Resolution: 1.65→27.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3734 0 29 392 4155
Biso mean--18.25 30.43 -
Num. residues----487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183981
X-RAY DIFFRACTIONf_angle_d1.55453
X-RAY DIFFRACTIONf_chiral_restr0.104620
X-RAY DIFFRACTIONf_plane_restr0.01718
X-RAY DIFFRACTIONf_dihedral_angle_d5.3582367
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 (%)
1.6501-1.69130.21961390.19384988512796
1.6913-1.7370.21441390.18434995513497
1.737-1.78810.21611400.17885057519797
1.7881-1.84590.21911410.17575092523397
1.8459-1.91180.18461430.16475108525198
1.9118-1.98830.16471390.15355038517798
1.9883-2.07880.1721420.15435099524198
2.0788-2.18840.18131420.1585144528699
2.1884-2.32540.14781460.155552355381100
2.3254-2.50480.21521450.164551855330100
2.5048-2.75670.18761440.175216536099
2.7567-3.15510.19451450.174652175362100
3.1551-3.97330.18261460.162252535399100
3.9733-27.83110.18141490.160953515500100

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