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- PDB-5evy: Salicylate hydroxylase substrate complex -

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Basic information

Entry
Database: PDB / ID: 5evy
TitleSalicylate hydroxylase substrate complex
ComponentsSalicylate hydroxylase
KeywordsOXIDOREDUCTASE / Complex / Monooxygenase
Function / homology
Function and homology information


salicylate 1-monooxygenase / secondary metabolite biosynthetic process / FAD binding / monooxygenase activity
Similarity search - Function
Salicylate 1-monooxygenase / : / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 2-HYDROXYBENZOIC ACID / Salicylate 1-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsMorimoto, Y. / Uemura, T.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: The catalytic mechanism of decarboxylative hydroxylation of salicylate hydroxylase revealed by crystal structure analysis at 2.5 angstrom resolution
Authors: Uemura, T. / Kita, A. / Watanabe, Y. / Adachi, M. / Kuroki, R. / Morimoto, Y.
History
DepositionNov 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Salicylate hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1163
Polymers47,1921
Non-polymers9242
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-9 kcal/mol
Surface area17180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.330, 142.330, 62.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Salicylate hydroxylase


Mass: 47192.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: sal / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q59713, salicylate 1-monooxygenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 68.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: ammonium sulfate, lithium sulfate, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Jan 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.47→43.83 Å / Num. obs: 26083 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 12
Reflection shellResolution: 2.47→2.6 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Cootmodel building
MOSFLMdata collection
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→37.32 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.858 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26017 1324 5.1 %RANDOM
Rwork0.20084 ---
obs0.20385 24736 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.152 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å2-0 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.47→37.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3119 0 53 68 3240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193247
X-RAY DIFFRACTIONr_bond_other_d0.0010.023076
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.9734427
X-RAY DIFFRACTIONr_angle_other_deg0.87637060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8625409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91523.383133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.99615498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3671521
X-RAY DIFFRACTIONr_chiral_restr0.0940.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213670
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02731
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.2446.4311642
X-RAY DIFFRACTIONr_mcbond_other5.2366.4271641
X-RAY DIFFRACTIONr_mcangle_it7.7049.6282049
X-RAY DIFFRACTIONr_mcangle_other7.7039.6342050
X-RAY DIFFRACTIONr_scbond_it5.4396.841605
X-RAY DIFFRACTIONr_scbond_other5.4286.8361604
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.27410.0952379
X-RAY DIFFRACTIONr_long_range_B_refined12.04454.4153820
X-RAY DIFFRACTIONr_long_range_B_other12.0454.443815
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.47→2.534 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 89 -
Rwork0.327 1802 -
obs--100 %

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