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- PDB-2fn0: Crystal structure of Yersinia enterocolitica salicylate synthase ... -

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Basic information

Entry
Database: PDB / ID: 2fn0
TitleCrystal structure of Yersinia enterocolitica salicylate synthase (Irp9)
Componentssalicylate synthetase, Irp9
KeywordsTRANSCRIPTION / Yersinia enterocolitica / Irp9 / salicylate synthase / siderophore
Function / homology
Function and homology information


carbon-oxygen lyase activity / oxo-acid-lyase activity / isochorismate synthase activity / siderophore biosynthetic process / L-tryptophan biosynthetic process / magnesium ion binding
Similarity search - Function
Salicylate synthase / Anthranilate synthase / Anthranilate synthase / Anthranilate synthase component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / : / Salicylate synthetase, Irp9
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKerbarh, O. / Chirgadze, D.Y. / Blundell, T.L. / Abell, C.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structures of Yersinia enterocolitica Salicylate Synthase and its Complex with the Reaction Products Salicylate and Pyruvate.
Authors: Kerbarh, O. / Chirgadze, D.Y. / Blundell, T.L. / Abell, C.
History
DepositionJan 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 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_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_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

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Assembly

Deposited unit
A: salicylate synthetase, Irp9
B: salicylate synthetase, Irp9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9748
Polymers96,6182
Non-polymers3576
Water9,908550
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-50 kcal/mol
Surface area29870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.740, 145.671, 58.807
Angle α, β, γ (deg.)90.00, 107.97, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is the dimer present in the asymmetric unit

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Components

#1: Protein salicylate synthetase, Irp9


Mass: 48308.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Strain: 8081 / Gene: IRP9 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(D3) / References: GenBank: 5420055, UniProt: Q9X9I8*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M magnesium acetate tetrahydrate, 0.1M sodium cacodylate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 23, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 77309 / Num. obs: 72593 / % possible obs: 93.9 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Redundancy: 3.8 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 16.1
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.306 / Num. unique all: 5176 / Rsym value: 0.306 / % possible all: 87.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
X-GENdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: composite search probe from 1QDL, 1I7Q and 1I1Q

1qdl

1i7q

1i1q


Resolution: 1.85→28.17 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.103 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.147 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24035 3649 5 %RANDOM
Rwork0.18717 ---
all0.18988 73421 --
obs0.18988 68906 93.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.577 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.03 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.85→28.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6318 0 20 550 6888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226462
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9578783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4115831
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79623.474285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.487151045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4321555
X-RAY DIFFRACTIONr_chiral_restr0.1060.2987
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024956
X-RAY DIFFRACTIONr_nbd_refined0.2020.23072
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24409
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.2527
X-RAY DIFFRACTIONr_metal_ion_refined0.070.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.26
X-RAY DIFFRACTIONr_mcbond_it3.26154240
X-RAY DIFFRACTIONr_mcangle_it4.0866600
X-RAY DIFFRACTIONr_scbond_it3.83952520
X-RAY DIFFRACTIONr_scangle_it5.297.52183
LS refinement shellResolution: 1.85→1.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 236 -
Rwork0.245 4739 -
obs-4975 87.04 %

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