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- PDB-3o82: Structure of BasE N-terminal domain from Acinetobacter baumannii ... -

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Basic information

Entry
Database: PDB / ID: 3o82
TitleStructure of BasE N-terminal domain from Acinetobacter baumannii bound to 5'-O-[N-(2,3-dihydroxybenzoyl)sulfamoyl] adenosine
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 ...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 / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HP8 / Peptide arylation enzyme / Peptide arylation enzyme
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.2Sep 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 / software / struct_conn / struct_ncs_dom_lim / 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 / _software.name / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)122,8628
Polymers121,7372
Non-polymers1,1256
Water88349
1
A: Peptide arylation enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4314
Polymers60,8681
Non-polymers5633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptide arylation enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4314
Polymers60,8681
Non-polymers5633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-44 kcal/mol
Surface area33680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.447, 145.259, 149.063
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 5 - 435 / Label seq-ID: 7 - 437

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#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
#2: Chemical ChemComp-HP8 / 5'-O-{[(2,3-dihydroxyphenyl)carbonyl]sulfamoyl}adenosine / 5'-O-[N-(2,3-dihydroxybenzoyl)sulfamoyl] adenosine


Mass: 482.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18N6O9S
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
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: 2.91 Å3/Da / Density % sol: 57.73 %
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: BL9-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2008
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal; asymetric cut 12.2 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 39977 / Num. obs: 38979 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 56.6 Å2 / Rsym value: 0.131 / Net I/σ(I): 9.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.377 / % possible all: 81.9

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Processing

Software
NameVersionClassification
Web-Icedata collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MDB residues 1-430

1mdb


Resolution: 2.7→40 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.896 / SU B: 10.586 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.475 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25128 1966 5.1 %RANDOM
Rwork0.20028 ---
obs0.20285 36904 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 57.064 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å2-0 Å2-0 Å2
2--1.97 Å20 Å2
3----3.24 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6762 0 70 49 6881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226991
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.9699533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4355868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.50824.396323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.143151097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4431539
X-RAY DIFFRACTIONr_chiral_restr0.1110.21068
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215383
X-RAY DIFFRACTIONr_mcbond_it0.8391.54338
X-RAY DIFFRACTIONr_mcangle_it1.62826995
X-RAY DIFFRACTIONr_scbond_it2.26132653
X-RAY DIFFRACTIONr_scangle_it3.8284.52538
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3323 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.310.5
MEDIUM THERMAL1.022
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 113 -
Rwork0.276 2230 -
obs-2230 81.3 %

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