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- PDB-6e97: Crystal structure of the aryl acid adenylating enzyme FscC from F... -

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Basic information

Entry
Database: PDB / ID: 6.0E+97
TitleCrystal structure of the aryl acid adenylating enzyme FscC from Fuscachelin NRPS in complex with DHB-adenylate
Components2,3-dihydroxybenzoate-AMP ligase
KeywordsLIGASE / siderophore biosynthesis / adenylation domain / dihydroxybenzoic acid activating enzyme
Function / homology
Function and homology information


2,3-dihydroxybenzoate--[aryl-carrier protein] ligase / siderophore biosynthetic process / ligase activity
Similarity search - Function
2,3-dihydroxybenzoate-AMP ligase / ANL, C-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily ...2,3-dihydroxybenzoate-AMP ligase / ANL, C-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-J2J / 2,3-dihydroxybenzoate-AMP ligase
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBruner, S.D. / Zagulyaeva, A.A.
CitationJournal: To Be Published
Title: Implication of MbtH-like proteins in crystallization of the independent NRPS A domains. Crystal structure of FscC: supporting rationale for revised mechanism of freestanding aryl acid adenylating enzymes
Authors: Bruner, S.D. / Zagulyaeva, A.A.
History
DepositionJul 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Structure summary
Category: citation / struct / Item: _citation.title / _struct.title
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: 2,3-dihydroxybenzoate-AMP ligase
B: 2,3-dihydroxybenzoate-AMP ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,6486
Polymers119,4932
Non-polymers1,1554
Water10,593588
1
A: 2,3-dihydroxybenzoate-AMP ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3263
Polymers59,7461
Non-polymers5792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2,3-dihydroxybenzoate-AMP ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3223
Polymers59,7461
Non-polymers5752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)206.127, 51.327, 111.363
Angle α, β, γ (deg.)90.000, 119.880, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 2,3-dihydroxybenzoate-AMP ligase


Mass: 59746.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Strain: YX / Gene: Tfu_1871 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q47NR5
#2: Chemical ChemComp-J2J / 5'-O-[(S)-[(2,3-dihydroxybenzene-1-carbonyl)oxy](hydroxy)phosphoryl]adenosine


Mass: 483.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C17H18N5O10P / Details: Missin residues were not resolved
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 588 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG10000, lithium sulfate, Tris-HCl

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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: Mar 21, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 93921 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.103 / Χ2: 2.221 / Net I/σ(I): 8.5 / Num. measured all: 674977
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.8-1.836.70.56246611.28199.2
1.83-1.8670.47946061.333199.9
1.86-1.96.90.42246571.451199.5
1.9-1.9470.36146561.614199.9
1.94-1.9870.32746851.66199.7
1.98-2.0370.29746291.828199.9
2.03-2.0870.25846671.91199.8
2.08-2.137.10.22947092.097199.9
2.13-2.27.20.20646392.183199.9
2.2-2.277.20.18346712.2821100
2.27-2.357.30.16647042.2451100
2.35-2.447.30.15846892.3451100
2.44-2.557.40.14746882.4771100
2.55-2.697.50.12947012.5371100
2.69-2.867.50.11647182.681100
2.86-3.087.40.10446862.9091100
3.08-3.397.40.08647482.9791100
3.39-3.887.40.06947353.0251100
3.88-4.887.40.05547762.7961100
4.88-507.10.05148962.376199.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MDB

1mdb


Resolution: 1.8→41.67 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.7
RfactorNum. reflection% reflection
Rfree0.2166 2070 2.21 %
Rwork0.1836 --
obs0.1942 93761 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.76 Å2 / Biso mean: 21.6121 Å2 / Biso min: 7.51 Å2
Refinement stepCycle: final / Resolution: 1.8→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8272 0 119 588 8979
Biso mean--21.62 25.4 -
Num. residues----1072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058571
X-RAY DIFFRACTIONf_angle_d0.73111697
X-RAY DIFFRACTIONf_chiral_restr0.0481304
X-RAY DIFFRACTIONf_plane_restr0.0051548
X-RAY DIFFRACTIONf_dihedral_angle_d11.7135100
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 (%)
1.8009-1.8460.32621400.28856332647295
1.846-1.89590.28141440.26396498664298
1.8959-1.95160.30221430.24286480662398
1.9516-2.01460.27511400.23236493663398
2.0146-2.08650.2451470.22426525667298
2.0865-2.170.25211350.2166527666298
2.17-2.26870.24791410.21226532667398
2.2687-2.38820.22441430.21056526666998
2.3882-2.53770.26521470.21356574672198
2.5377-2.73330.23931370.20036552668998
2.7333-3.00790.23111460.19156614676098
3.0079-3.44190.21231460.17526580672698
3.4419-4.33190.18561450.15256632677798
4.3319-23.30420.1831510.16156786693798

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