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- PDB-3o84: Structure of BasE N-terminal domain from Acinetobacter baumannii ... -

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Basic information

Entry
Database: PDB / ID: 3o84
TitleStructure of BasE N-terminal domain from Acinetobacter baumannii bound to 6-phenyl-1-(pyridin-4-ylmethyl)-1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid.
ComponentsPeptide arylation enzyme
KeywordsLIGASE / Adenylation of 2 / 3-dihydroxybenzoate and transfer to pantetheine cofactor of BasF / Non-Ribosomal Peptide Synthetase (NRPS)
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-HTJ / TRIETHYLENE GLYCOL / Peptide arylation enzyme / Peptide arylation enzyme
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsDrake, E.J. / Duckworth, B.P. / Neres, J. / Aldrich, C.C. / Gulick, A.M.
CitationJournal: Biochemistry / Year: 2010
Title: Biochemical and structural characterization of bisubstrate inhibitors of BasE, the self-standing nonribosomal peptide synthetase adenylate-forming enzyme of acinetobactin synthesis.
Authors: Drake, E.J. / Duckworth, B.P. / Neres, J. / Aldrich, C.C. / Gulick, A.M.
History
DepositionAug 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Sep 6, 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_ref_seq_dif / 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_ref_seq_dif.details / _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)122,94411
Polymers121,7372
Non-polymers1,2089
Water7,819434
1
A: Peptide arylation enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4376
Polymers60,8681
Non-polymers5695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptide arylation enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5075
Polymers60,8681
Non-polymers6394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-55 kcal/mol
Surface area34110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.534, 143.312, 148.815
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 / Fragment: BasE / Mutation: P45L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: AB900 / Gene: ACICU_02578, basE / Plasmid: pED453 / 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 , 6 types, 443 molecules

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


Mass: 330.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H14N4O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / 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: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.87 Å3/Da / Density % sol: 57.15 %
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: CHESS / Beamline: A1 / Wavelength: 0.9782 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 24, 2009
RadiationMonochromator: horizontal focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 82723 / Num. obs: 82475 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 32.3 Å2 / Rsym value: 0.072 / Net I/σ(I): 10.8
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.34 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 10447 / Rsym value: 0.425 / % possible all: 97.9

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Processing

Software
NameVersionClassification
AdxvPackagedata processing
MOLREPphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3O83

3o83


Resolution: 2.1→29.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.567 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 4086 5 %RANDOM
Rwork0.18521 ---
all0.1865 78200 --
obs0.1865 78200 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.368 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å2-0 Å2-0 Å2
2--0.67 Å20 Å2
3----2.07 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6778 0 80 434 7292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227027
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.979570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7055872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.43624.465327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.834151114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1391539
X-RAY DIFFRACTIONr_chiral_restr0.0780.21065
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215419
X-RAY DIFFRACTIONr_mcbond_it0.6241.54342
X-RAY DIFFRACTIONr_mcangle_it1.19627012
X-RAY DIFFRACTIONr_scbond_it1.73532685
X-RAY DIFFRACTIONr_scangle_it3.0024.52555
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 274 -
Rwork0.265 5523 -
obs--96.97 %

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