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- PDB-3u17: Structure of BasE N-terminal domain from Acinetobacter baumannii ... -

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Basic information

Entry
Database: PDB / ID: 3u17
TitleStructure of BasE N-terminal domain from Acinetobacter baumannii bound to 6-(p-benzoyl)phenyl-1-(pyridin-4-ylmethyl)-1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid
ComponentsPeptide arylation enzyme
KeywordsLIGASE / ANL Superfamily / adenylating enzyme / 2 / 3-dihydroxybenzoate:Aryl Carrier protein ligase / BasF
Function / homology
Function and homology information


2,3-dihydroxybenzoate--[aryl-carrier protein] ligase / siderophore biosynthetic process
Similarity search - Function
2,3-dihydroxybenzoate-AMP ligase / ANL, N-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. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme ...2,3-dihydroxybenzoate-AMP ligase / ANL, N-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. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-H90 / Peptide arylation enzyme / Peptide arylation enzyme
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsGulick, A.M. / Drake, E.J. / Aldrich, C.C. / Neres, J.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Non-nucleoside inhibitors of BasE, an adenylating enzyme in the siderophore biosynthetic pathway of the opportunistic pathogen Acinetobacter baumannii.
Authors: Neres, J. / Engelhart, C.A. / Drake, E.J. / Wilson, D.J. / Fu, P. / Boshoff, H.I. / Barry 3rd, C.E. / Gulick, A.M. / Aldrich, C.C.
History
DepositionSep 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2May 13, 2020Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ref_seq_dif.details
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide arylation enzyme
B: Peptide arylation enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,12213
Polymers121,7372
Non-polymers1,38611
Water6,864381
1
A: Peptide arylation enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5817
Polymers60,8681
Non-polymers7136
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptide arylation enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5416
Polymers60,8681
Non-polymers6735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-90 kcal/mol
Surface area33410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.368, 144.232, 148.735
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Peptide arylation enzyme


Mass: 60868.270 Da / Num. of mol.: 2 / Mutation: P45L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: Strain AB900 / Gene: ACICU_02578, basE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B2HVG8, UniProt: A0A7U3Y1M5*PLUS, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases

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Non-polymers , 5 types, 392 molecules

#2: Chemical ChemComp-H90 / 6-(4-benzoylphenyl)-1-(pyridin-4-ylmethyl)-1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid


Mass: 434.446 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H18N4O3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS ENTRY USES A UNIPROT REFERENCE THAT IS FOR A DIFFERENT STRAIN OF A. BAUMANNI. THESE CHANGES ...THIS ENTRY USES A UNIPROT REFERENCE THAT IS FOR A DIFFERENT STRAIN OF A. BAUMANNI. THESE CHANGES ARE STRAIN RELATED DIFFERENCES AS FOUND IN GENBANK ENTRY ZP_04661818.

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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: 2.88 Å3/Da / Density % sol: 57.29 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5-15% PEG 8000, 5% MPD, 250-600 MM CaCl2, 50 MM BTP , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 24, 2010
RadiationMonochromator: SSRL 11-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 82870 / Num. obs: 74749 / % possible obs: 90.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.1
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.278 / % possible all: 51.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.5_2)refinement
REFMAC(Diff. Fourier)refinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC(Diff. Fourier)phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3O84

3o84


Resolution: 2.1→40 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 25.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 3723 4.99 %Random
Rwork0.1885 ---
obs0.1901 74645 90.12 %-
all-82828 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.216 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.4535 Å20 Å2-0 Å2
2--2.6738 Å2-0 Å2
3----15.1273 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6756 0 89 381 7226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077017
X-RAY DIFFRACTIONf_angle_d1.0479564
X-RAY DIFFRACTIONf_dihedral_angle_d18.9542497
X-RAY DIFFRACTIONf_chiral_restr0.0681064
X-RAY DIFFRACTIONf_plane_restr0.0051251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.12680.3069660.26381327X-RAY DIFFRACTION46
2.1268-2.15480.3018810.25151511X-RAY DIFFRACTION53
2.1548-2.18430.3004820.25421750X-RAY DIFFRACTION60
2.1843-2.21550.2691020.24791874X-RAY DIFFRACTION66
2.2155-2.24860.27531050.2382031X-RAY DIFFRACTION70
2.2486-2.28370.30351160.23152185X-RAY DIFFRACTION76
2.2837-2.32120.28641340.23052350X-RAY DIFFRACTION82
2.3212-2.36120.2581360.22442561X-RAY DIFFRACTION88
2.3612-2.40410.24841360.22392676X-RAY DIFFRACTION93
2.4041-2.45040.30811340.22242810X-RAY DIFFRACTION98
2.4504-2.50040.27861360.21712906X-RAY DIFFRACTION99
2.5004-2.55470.23651600.21682859X-RAY DIFFRACTION100
2.5547-2.61420.26441590.22112908X-RAY DIFFRACTION100
2.6142-2.67950.27591470.21442856X-RAY DIFFRACTION100
2.6795-2.7520.29221360.21952935X-RAY DIFFRACTION100
2.752-2.83290.26491710.20742887X-RAY DIFFRACTION100
2.8329-2.92440.26171580.20732883X-RAY DIFFRACTION100
2.9244-3.02890.26751480.19872901X-RAY DIFFRACTION100
3.0289-3.15010.25441630.19122929X-RAY DIFFRACTION100
3.1501-3.29340.21391650.19772908X-RAY DIFFRACTION100
3.2934-3.4670.22161380.17292930X-RAY DIFFRACTION100
3.467-3.68410.17881590.15692930X-RAY DIFFRACTION100
3.6841-3.96840.16311640.14442926X-RAY DIFFRACTION100
3.9684-4.36750.15881550.13962963X-RAY DIFFRACTION100
4.3675-4.99880.14831560.14172968X-RAY DIFFRACTION100
4.9988-6.29540.21331530.183009X-RAY DIFFRACTION100
6.2954-45.75760.2121630.20213149X-RAY DIFFRACTION100

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