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- PDB-5jy9: An iron-bound structure of the salicylate synthase Irp9 -

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Basic information

Entry
Database: PDB / ID: 5jy9
TitleAn iron-bound structure of the salicylate synthase Irp9
ComponentsPutative salicylate synthetase
KeywordsISOMERASE / chorismate / isochorismate
Function / homology
Function and homology information


oxo-acid-lyase activity / isochorismate synthase activity / L-tryptophan biosynthetic process / metal 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 / : / Salicylate synthetase
Similarity search - Component
Biological speciesYersinia enterocolitica serotype O:8 / biotype 1B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.162 Å
AuthorsMeneely, K.M. / Lamb, A.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI77725 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K02 AI093675 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: An Open and Shut Case: The Interaction of Magnesium with MST Enzymes.
Authors: Meneely, K.M. / Sundlov, J.A. / Gulick, A.M. / Moran, G.R. / Lamb, A.L.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative salicylate synthetase
B: Putative salicylate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5008
Polymers96,1152
Non-polymers3856
Water2,756153
1
A: Putative salicylate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2324
Polymers48,0581
Non-polymers1743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative salicylate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2694
Polymers48,0581
Non-polymers2113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.392, 145.351, 58.437
Angle α, β, γ (deg.)90.00, 108.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative salicylate synthetase


Mass: 48057.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081) (bacteria)
Strain: NCTC 13174 / 8081 / Gene: ybtS, YE2612 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) pLysS / References: UniProt: A1JTF3
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 14% PEG 8 000, 0.25 M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.739 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 2015 / Details: Mirror: Rh coated flat mirror
RadiationMonochromator: Si(111) side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.739 Å / Relative weight: 1
ReflectionResolution: 2.16→39.12 Å / Num. obs: 47172 / % possible obs: 98.9 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rsym value: 0.096 / Net I/σ(I): 18.3
Reflection shellResolution: 2.16→2.23 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 3 / % possible all: 88.1

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FN1

2fn1


Resolution: 2.162→36.519 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 23.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 2359 5 %Random selection
Rwork0.172 ---
obs0.1751 47138 98.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.16 Å2
Refinement stepCycle: LAST / Resolution: 2.162→36.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6421 0 19 153 6593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136559
X-RAY DIFFRACTIONf_angle_d1.2148885
X-RAY DIFFRACTIONf_dihedral_angle_d13.5513959
X-RAY DIFFRACTIONf_chiral_restr0.06992
X-RAY DIFFRACTIONf_plane_restr0.0081164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.162-2.20610.29151120.22472205X-RAY DIFFRACTION84
2.2061-2.2540.29881460.21442626X-RAY DIFFRACTION97
2.254-2.30650.2751260.19442597X-RAY DIFFRACTION100
2.3065-2.36410.2841610.19432651X-RAY DIFFRACTION100
2.3641-2.4280.26511810.19152618X-RAY DIFFRACTION100
2.428-2.49950.26041310.18462658X-RAY DIFFRACTION100
2.4995-2.58010.25671070.18232687X-RAY DIFFRACTION100
2.5801-2.67230.25231200.18892689X-RAY DIFFRACTION100
2.6723-2.77930.27581540.18922645X-RAY DIFFRACTION100
2.7793-2.90570.26121780.19142627X-RAY DIFFRACTION100
2.9057-3.05880.23371180.18642685X-RAY DIFFRACTION100
3.0588-3.25040.29471330.18262685X-RAY DIFFRACTION100
3.2504-3.50120.261200.18252662X-RAY DIFFRACTION100
3.5012-3.85310.2121310.15882678X-RAY DIFFRACTION100
3.8531-4.40990.20671570.14452672X-RAY DIFFRACTION100
4.4099-5.55290.14091140.12942717X-RAY DIFFRACTION100
5.5529-36.52450.21041700.17062677X-RAY DIFFRACTION100

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