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- PDB-4bk3: Crystal structure of 3-hydroxybenzoate 6-hydroxylase uncovers lip... -

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Basic information

Entry
Database: PDB / ID: 4bk3
TitleCrystal structure of 3-hydroxybenzoate 6-hydroxylase uncovers lipid- assisted flavoprotein strategy for regioselective aromatic hydroxylation: Y105F mutant
ComponentsPROBABLE SALICYLATE MONOOXYGENASE
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / GENTISATE / HYDROXYLASE / MONOOXYGENASE / 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 / MOLECULAR REPLACEMENT / Resolution: 1.78 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 1.3Dec 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 / 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

Downloads & links

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Assembly

Deposited unit
A: PROBABLE SALICYLATE MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6625
Polymers46,9321
Non-polymers1,7294
Water5,350297
1
A: PROBABLE SALICYLATE MONOOXYGENASE
hetero molecules

A: PROBABLE SALICYLATE MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,32310
Polymers93,8642
Non-polymers3,4598
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
Buried area7560 Å2
ΔGint-75.3 kcal/mol
Surface area30170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.410, 106.410, 142.620
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-2041-

HOH

21A-2051-

HOH

31A-2052-

HOH

41A-2090-

HOH

51A-2269-

HOH

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Components

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


Mass: 46932.242 Da / Num. of mol.: 1 / Mutation: YES
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.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 42.99 % / Description: NONE
Crystal growpH: 8.5
Details: 30% PEG 4000, 0.2 M LISO4 AND 0.1 M TRIS/HCL (PH 8.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.78→45.14 Å / Num. obs: 39090 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.5
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0033refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BJY

4bjy


Resolution: 1.78→85.29 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.64 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.20498 1938 5 %RANDOM
Rwork0.1589 ---
obs0.16118 37128 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.366 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.78→85.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3077 0 99 297 3473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193262
X-RAY DIFFRACTIONr_bond_other_d0.0010.023010
X-RAY DIFFRACTIONr_angle_refined_deg1.9741.9754431
X-RAY DIFFRACTIONr_angle_other_deg0.93236910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4075396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17723.185157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71815496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0611530
X-RAY DIFFRACTIONr_chiral_restr0.1220.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023702
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02775
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 1.782→1.828 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 147 -
Rwork0.233 2729 -
obs--99.9 %
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)
11.2408-0.36250.67441.47950.0351.6627-0.0454-0.02570.2097-0.2878-0.06350.0419-0.1662-0.07680.10890.09460.0424-0.02520.0410.02120.12624.2967.4935.016
20.9758-0.05690.42850.62310.01731.3339-0.0355-0.16550.2316-0.0573-0.06280.1125-0.0704-0.24020.09830.02110.0342-0.01920.0782-0.04060.135624.8554.37718.687
32.5313-0.24990.43112.75820.81882.07640.0756-0.55930.04340.1076-0.17060.41060.169-0.55380.0950.0239-0.06710.03440.3271-0.04150.113117.234-6.26333.637
40.5904-0.10420.53340.4668-0.02251.50360.0374-0.01340.0648-0.096-0.04880.00420.0070.02510.01140.04940.0127-0.0040.03880.00720.05135.577-3.10413.613
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 60
2X-RAY DIFFRACTION2A61 - 232
3X-RAY DIFFRACTION3A233 - 276
4X-RAY DIFFRACTION4A277 - 398

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