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- PDB-1md9: CRYSTAL STRUCTURE OF DhbE IN COMPLEX WITH DHB AND AMP -

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Basic information

Entry
Database: PDB / ID: 1md9
TitleCRYSTAL STRUCTURE OF DhbE IN COMPLEX WITH DHB AND AMP
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
ADENOSINE MONOPHOSPHATE / 2,3-DIHYDROXY-BENZOIC ACID / 2,3-dihydroxybenzoate-AMP ligase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.8 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 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / 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)60,8653
Polymers60,3631
Non-polymers5012
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.900, 66.900, 114.800
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: 60363.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: M15 ATCC 21332 / Production host: Escherichia coli (E. coli)
References: UniProt: P40871, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-DBH / 2,3-DIHYDROXY-BENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.92 %
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 23, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 13234 / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 14081 / % possible obs: 95 % / Num. measured all: 38167 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 90.9 % / Rmerge(I) obs: 0.102 / Mean I/σ(I) obs: 12.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→100 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.288 -RANDOM
Rwork0.232 --
obs-13234 -
Refinement stepCycle: LAST / Resolution: 2.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4198 0 0 0 4198
Refinement
*PLUS
Highest resolution: 2.8 Å / Rfactor Rfree: 0.288 / Rfactor Rwork: 0.232 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.0085
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.48

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