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- PDB-1mdf: CRYSTAL STRUCTURE OF DhbE IN ABSENCE OF SUBSTRATE -

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Basic information

Entry
Database: PDB / ID: 1mdf
TitleCRYSTAL STRUCTURE OF DhbE IN ABSENCE OF SUBSTRATE
Components2,3-dihydroxybenzoate-AMP ligase
KeywordsLIGASE / adenylation domain / peptide synthetase / antibiotic biosynthesis / siderophore formation
Function / homology
Function and homology information


2,3-dihydroxybenzoate-[aryl-carrier protein] ligase / 2,3-dihydroxybenzoate--[aryl-carrier protein] ligase / siderophore biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
2,3-dihydroxybenzoate-AMP ligase / Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / : / ANL, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. ...2,3-dihydroxybenzoate-AMP ligase / Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / : / ANL, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / Roll / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
2,3-dihydroxybenzoate-AMP ligase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMay, J.J. / Kessler, N. / Marahiel, M.A. / Stubbs, M.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Crystal structure of DhbE, an archetype for aryl acid activating domains of modular nonribosomal peptide synthetases.
Authors: May, J.J. / Kessler, N. / Marahiel, M.A. / Stubbs, M.T.
History
DepositionAug 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Author states the sequence has recently been deposited at NCBI with the acquisition number ...SEQUENCE Author states the sequence has recently been deposited at NCBI with the acquisition number bankit484943.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2,3-dihydroxybenzoate-AMP ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1803
Polymers59,9881
Non-polymers1922
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.450, 65.450, 106.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein 2,3-dihydroxybenzoate-AMP ligase / DHBE / Dihydroxybenzoic acid-activating enzyme


Mass: 59988.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: ATCC 21332 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 pREP4
References: UniProt: P40871, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8.6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprotein1drop
230 %PEG40001reservoir
30.1 MTris-HCl1reservoir
40.2 M1reservoirpH8.6Li2SO4

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Data collection

DetectorDate: Mar 10, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 16523 / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 17099 / % possible obs: 96.5 % / Num. measured all: 42630 / Rmerge(I) obs: 0.088
Reflection shell
*PLUS
% possible obs: 92.4 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.68

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MD9

1md9


Resolution: 2.5→100 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.275 -RANDOM
Rwork0.204 --
obs-16523 -
Refinement stepCycle: LAST / Resolution: 2.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4198 0 10 93 4301
Refinement
*PLUS
Rfactor Rfree: 0.275 / Rfactor Rwork: 0.204 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.0063
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.35

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