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- PDB-3u16: Structure of BasE N-terminal domain from Acinetobacter baumannii ... -

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Basic information

Entry
Database: PDB / ID: 3u16
TitleStructure of BasE N-terminal domain from Acinetobacter baumannii bound to 6-(p-benzyloxy)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-H89 / 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_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_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.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)123,08612
Polymers121,7372
Non-polymers1,35010
Water9,206511
1
A: Peptide arylation enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5837
Polymers60,8681
Non-polymers7156
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptide arylation enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5035
Polymers60,8681
Non-polymers6354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-82 kcal/mol
Surface area33450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.093, 144.780, 148.675
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: 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, 521 molecules

#2: Chemical ChemComp-H89 / 6-[4-(benzyloxy)phenyl]-1-(pyridin-4-ylmethyl)-1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid


Mass: 436.462 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H20N4O3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / 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.: 511 / 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: 2.92 Å3/Da / Density % sol: 57.9 %
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: 84673 / Num. obs: 82980 / % possible obs: 98 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.8
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.542 / % possible all: 88.4

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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→39.65 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 23.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 4087 4.96 %Random
Rwork0.1849 ---
obs0.1866 82408 98.08 %-
all-84090 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.47 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.6109 Å20 Å2-0 Å2
2--1.4534 Å2-0 Å2
3----12.0643 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6774 0 88 511 7373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077054
X-RAY DIFFRACTIONf_angle_d1.0589613
X-RAY DIFFRACTIONf_dihedral_angle_d18.3372516
X-RAY DIFFRACTIONf_chiral_restr0.0691067
X-RAY DIFFRACTIONf_plane_restr0.0051257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12470.31871200.26752317X-RAY DIFFRACTION85
2.1247-2.15060.29891170.2682462X-RAY DIFFRACTION90
2.1506-2.17780.2841320.24772472X-RAY DIFFRACTION92
2.1778-2.20650.29371340.25242595X-RAY DIFFRACTION95
2.2065-2.23670.26891350.22482582X-RAY DIFFRACTION96
2.2367-2.26870.26161340.22682671X-RAY DIFFRACTION97
2.2687-2.30250.27451590.21692631X-RAY DIFFRACTION98
2.3025-2.33850.27431350.20762730X-RAY DIFFRACTION99
2.3385-2.37680.23291400.20462690X-RAY DIFFRACTION99
2.3768-2.41780.27631370.20842686X-RAY DIFFRACTION99
2.4178-2.46180.29521310.19392724X-RAY DIFFRACTION99
2.4618-2.50910.23441260.18862741X-RAY DIFFRACTION100
2.5091-2.56030.21321500.17932742X-RAY DIFFRACTION100
2.5603-2.6160.23171340.19642716X-RAY DIFFRACTION100
2.616-2.67680.28371530.19992696X-RAY DIFFRACTION100
2.6768-2.74380.28621360.2062757X-RAY DIFFRACTION100
2.7438-2.81790.24681470.19262704X-RAY DIFFRACTION100
2.8179-2.90080.27861540.20252774X-RAY DIFFRACTION100
2.9008-2.99440.25321460.18872732X-RAY DIFFRACTION100
2.9944-3.10140.23941440.18732741X-RAY DIFFRACTION100
3.1014-3.22550.23051460.19522746X-RAY DIFFRACTION100
3.2255-3.37230.21011420.18162770X-RAY DIFFRACTION100
3.3723-3.54990.18471510.16422753X-RAY DIFFRACTION100
3.5499-3.77220.17511470.15052770X-RAY DIFFRACTION100
3.7722-4.06320.16711520.14922782X-RAY DIFFRACTION100
4.0632-4.47160.15711490.14162772X-RAY DIFFRACTION100
4.4716-5.11750.14871460.13832817X-RAY DIFFRACTION100
5.1175-6.4430.19231420.17722820X-RAY DIFFRACTION99
6.443-39.6570.20631480.18712928X-RAY DIFFRACTION98

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