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- PDB-5hym: 3-Hydroxybenzoate 6-hydroxylase from Rhodococcus jostii in comple... -

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Basic information

Entry
Database: PDB / ID: 5hym
Title3-Hydroxybenzoate 6-hydroxylase from Rhodococcus jostii in complex with phosphatidylinositol
ComponentsProbable salicylate monooxygenase
KeywordsOXIDOREDUCTASE / flavoprotein / monooxygenase / phospholipid / Rhodococcus
Function / homology
Function and homology information


salicylate 1-monooxygenase / salicylate 1-monooxygenase activity / 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 / Phosphatidylinositol / Probable salicylate monooxygenase
Similarity search - Component
Biological speciesRhodococcus jostii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsOrru, R. / Montersino, S. / Mattevi, A. / van Berkel, W.J.H.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research Netherlands
CitationJournal: Front Microbiol / Year: 2017
Title: 3-Hydroxybenzoate 6-Hydroxylase from Rhodococcus jostii RHA1 Contains a Phosphatidylinositol Cofactor.
Authors: Montersino, S. / Te Poele, E. / Orru, R. / Westphal, A.H. / Barendregt, A. / Heck, A.J.R. / van der Geize, R. / Dijkhuizen, L. / Mattevi, A. / van Berkel, W.J.H.
History
DepositionFeb 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)48,6564
Polymers46,9481
Non-polymers1,7083
Water25214
1
A: Probable salicylate monooxygenase
hetero molecules

A: Probable salicylate monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3138
Polymers93,8962
Non-polymers3,4166
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area4520 Å2
ΔGint-43 kcal/mol
Surface area30890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.980, 106.980, 143.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-612-

HOH

21A-614-

HOH

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Components

#1: Protein Probable salicylate monooxygenase


Mass: 46948.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus jostii (strain RHA1) (bacteria)
Gene: RHA1_ro01869 / Plasmid: Q2+ / Production host: Rhodococcus jostii (bacteria) / Strain (production host): RHA1 #2 / References: UniProt: Q0SFK6, salicylate 1-monooxygenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-T7X / Phosphatidylinositol / Phosphatidylinositol


Mass: 887.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H83O13P
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 4000, 0.2 M lithium sulphate, 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: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→43.64 Å / Num. obs: 18766 / % possible obs: 99.7 % / Redundancy: 7.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.061 / Rrim(I) all: 0.172 / Net I/σ(I): 8.4 / Num. measured all: 140686 / Scaling rejects: 189
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.3-2.385.80.5471100
8.91-43.644.30.08193.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.74 Å43.64 Å
Translation6.74 Å43.64 Å

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Processing

Software
NameVersionClassification
MOSFLM7.2.1data reduction
Aimless0.5.21data scaling
PHASER2.6.1phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BJZ

4bjz


Resolution: 2.3→43.64 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.2714 / WRfactor Rwork: 0.2128 / FOM work R set: 0.8084 / SU B: 8.098 / SU ML: 0.196 / SU R Cruickshank DPI: 0.4044 / SU Rfree: 0.2648 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.404 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2617 1337 7.1 %RANDOM
Rwork0.2059 ---
obs0.21 17415 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.62 Å2 / Biso mean: 33.408 Å2 / Biso min: 14.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0 Å2
2---0.35 Å20 Å2
3---0.7 Å2
Refinement stepCycle: final / Resolution: 2.3→43.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3078 0 106 14 3198
Biso mean--30.9 30.53 -
Num. residues----395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193260
X-RAY DIFFRACTIONr_bond_other_d0.0060.022989
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.9774430
X-RAY DIFFRACTIONr_angle_other_deg1.02536857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9445394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9423.185157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12115493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1751530
X-RAY DIFFRACTIONr_chiral_restr0.0970.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023708
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02779
X-RAY DIFFRACTIONr_mcbond_it2.4443.1771579
X-RAY DIFFRACTIONr_mcbond_other2.4443.1761578
X-RAY DIFFRACTIONr_mcangle_it3.8184.7561972
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 104 -
Rwork0.268 1250 -
all-1354 -
obs--99.93 %

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