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- PDB-4bjy: Crystal structure of 3-hydroxybenzoate 6-hydroxylase uncovers lip... -

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Basic information

Entry
Database: PDB / ID: 4bjy
TitleCrystal structure of 3-hydroxybenzoate 6-hydroxylase uncovers lipid- assisted flavoprotein strategy for regioselective aromatic hydroxylation: Platinum derivative
ComponentsPROBABLE SALICYLATE MONOOXYGENASE
KeywordsOXIDOREDUCTASE / GENTISATE / PHOSPHOLIPID
Function / homology
Function and homology information


salicylate 1-monooxygenase activity / salicylate 1-monooxygenase / FAD binding
Similarity search - Function
D-Amino Acid Oxidase; Chain A, domain 2 - #30 / : / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATIDYLGLYCEROL-PHOSPHOGLYCEROL / Probable salicylate monooxygenase
Similarity search - Component
Biological speciesRHODOCOCCUS JOSTII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å
AuthorsOrru, R. / Montersino, S. / Barendregt, A. / Westphal, A.H. / van Duijn, E. / Mattevi, A. / van Berkel, W.J.H.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal Structure of 3-Hydroxybenzoate 6-Hydroxylase Uncovers Lipid-Assisted Flavoprotein Strategy for Regioselective Aromatic Hydroxylation
Authors: Montersino, S. / Orru, R. / Barendregt, A. / Westphal, A.H. / Van Duijn, E. / Mattevi, A. / Van Berkel, W.J.H.
History
DepositionApr 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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: PROBABLE SALICYLATE MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6424
Polymers46,9481
Non-polymers1,6943
Water4,990277
1
A: PROBABLE SALICYLATE MONOOXYGENASE
hetero molecules

A: PROBABLE SALICYLATE MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2848
Polymers93,8962
Non-polymers3,3886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
Buried area7310 Å2
ΔGint-47.6 kcal/mol
Surface area30350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.610, 106.610, 142.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-2085-

HOH

21A-2094-

HOH

31A-2251-

HOH

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Components

#1: Protein PROBABLE SALICYLATE MONOOXYGENASE / 3-HYDROXYBENZOATE 6-HYDROXYLASE


Mass: 46948.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOCOCCUS JOSTII (bacteria) / Strain: RHA1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10
References: UniProt: Q0SFK6, salicylate 1-monooxygenase, EC: 1.14.13.24
#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-P3A / PHOSPHATIDYLGLYCEROL-PHOSPHOGLYCEROL


Mass: 872.997 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H78O15P2 / Comment: phospholipid*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPRESENCE OF 6XHIS TAG AT C-TERM

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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: 2.16 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growpH: 8.5
Details: 28% PEG 4000, 0.2 M SODIUM ACETATE AND 0.1 M TRIS-HCL (PH 8.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.52→53.3 Å / Num. obs: 62993 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 23.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 33.5
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 24.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 6.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0033refinement
MOSFLMdata reduction
Aimlessdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.52→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.197 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 197-198 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.20499 3168 5 %RANDOM
Rwork0.1735 ---
obs0.17507 59801 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: 19.123 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.52→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3062 0 98 277 3437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193246
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1041.9754408
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4685393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61223.141156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.8915493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6311530
X-RAY DIFFRACTIONr_chiral_restr0.1410.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212503
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4481.3451572
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1112.0141962
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4691.6081674
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.52→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 230 -
Rwork0.188 4342 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2168-0.17170.15110.2324-0.05730.3843-0.0095-0.01110.0372-0.059-0.01740.0192-0.05-0.06050.02690.04360.0179-0.03210.0192-0.00280.040423.36965.82136.0132
20.255-0.07430.10370.1336-0.09630.1382-0.0272-0.08940.028-0.01570.01760.03180.0053-0.07290.00950.00780.0094-0.01020.0657-0.02450.030523.8555-1.672528.7321
30.1065-0.06010.21330.1476-0.06620.4780.0076-0.0020.0009-0.0362-0.00420.0026-0.0040.0148-0.00340.02650.0016-0.00660.02760.00420.019937.6336-1.569314.985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 73
2X-RAY DIFFRACTION1A94 - 175
3X-RAY DIFFRACTION2A74 - 93
4X-RAY DIFFRACTION2A176 - 302
5X-RAY DIFFRACTION3A303 - 398

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