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- PDB-2x3j: CO-COMPLEX STRUCTURE OF ACHROMOBACTIN SYNTHETASE PROTEIN D (ACSD)... -

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Basic information

Entry
Database: PDB / ID: 2x3j
TitleCO-COMPLEX STRUCTURE OF ACHROMOBACTIN SYNTHETASE PROTEIN D (ACSD) WITH ATP AND N-CITRYL-ETHYLENEDIAMINE FROM PECTOBACTERIUM CHRYSANTHEMI
ComponentsACSD
KeywordsLIGASE / ALCALIGIN BIOSYNTHESIS / ALCC / ADENYLATION / SIDEROPHORES / IRON ACQUISITION
Function / homology
Function and homology information


acid-amino acid ligase activity / siderophore biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
PvsD/AcsD-like, thumb domain, helical bundle / PvsD/AcsD-like, thumb domain, four stranded beta-sheet / PvsD/AcsD-like, palm domain, helix bundle / Aerobactin siderophore biosynthesis, IucA/IucC, N-terminal / Aerobactin siderophore biosynthesis, IucA/IucC-like / IucA / IucC family / Ferric iron reductase FhuF domain / Ferric iron reductase FhuF-like transporter
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Chem-X3J / AcsD
Similarity search - Component
Biological speciesERWINIA CHRYSANTHEMI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchmelz, S. / Challis, G.L. / Naismith, J.H.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural Basis for Acyl Acceptor Specificity in the Achromobactin Biosynthetic Enzyme Acsd.
Authors: Schmelz, S. / Botting, C.H. / Song, L. / Kadi, N.F. / Challis, G.L. / Naismith, J.H.
History
DepositionJan 25, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references / Other / Version format compliance
Revision 1.2Sep 14, 2011Group: Database references
Revision 1.3Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.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_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_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_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
A: ACSD
B: ACSD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,95612
Polymers141,1982
Non-polymers1,75810
Water10,287571
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-43.1 kcal/mol
Surface area43570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.704, 71.521, 95.595
Angle α, β, γ (deg.)97.26, 101.97, 91.01
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ACSD


Mass: 70598.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ERWINIA CHRYSANTHEMI (bacteria) / Plasmid: PET151/D-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93AT8

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Non-polymers , 5 types, 581 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-X3J / (2S)-2-{2-[(2-AMINOETHYL)AMINO]-2-OXOETHYL}-2-HYDROXYBUTANEDIOIC ACID / 5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE


Mass: 234.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14N2O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H2O

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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: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: FOR CO-CRYSTALLIZATION WITH N-CITRYL-ETHYLENEDIAMINE 9 MG/ML WT ACSD (STORED IN PROTEIN BUFFER: 50 MM TRIS-HCL PH 7.5, 500 MM NACL, 10 % GLYCEROL) WAS INCUBATED FOR ONE HOUR WITH 15 MM ...Details: FOR CO-CRYSTALLIZATION WITH N-CITRYL-ETHYLENEDIAMINE 9 MG/ML WT ACSD (STORED IN PROTEIN BUFFER: 50 MM TRIS-HCL PH 7.5, 500 MM NACL, 10 % GLYCEROL) WAS INCUBATED FOR ONE HOUR WITH 15 MM ETHYLENEDIAMINE, 10 MM MGCL2, 15 MM ATP AND 15 MM CITRATE. THE SUPERNATANT WAS USED TO GROW N-CITRYL-ETHYLENEDIAMINE CO-COMPLEX CRYSTALS IN HANGING DROPS FROM EQUAL MIXTURES WITH 0.1 M HEPES PH 7.2, 17% PEG 8000, 7.5% (V/V) GLYCEROL AT 20C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorDate: Nov 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 89038 / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.7 / % possible all: 74.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FFE

3ffe


Resolution: 2→92.85 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.961 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23129 4680 5 %RANDOM
Rwork0.18994 ---
obs0.19204 89038 93.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.189 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-3.34 Å2-1.85 Å2
2--2.66 Å20.92 Å2
3----2.59 Å2
Refinement stepCycle: LAST / Resolution: 2→92.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9323 0 110 571 10004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0219852
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.95613429
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78151210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73223.287508
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.308151605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8271595
X-RAY DIFFRACTIONr_chiral_restr0.0840.21420
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027712
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.24798
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.26666
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2691
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.751.56069
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25629484
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.73334330
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7054.53922
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 267 -
Rwork0.26 5185 -
obs--73.43 %

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