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- PDB-3u52: X-ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase f... -

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Basic information

Entry
Database: PDB / ID: 3u52
TitleX-ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase from Pseudomonas sp. OX1
Components(Phenol hydroxylase component ...) x 3
KeywordsOXIDOREDUCTASE / 4-Helix Bundle / Hydroxylase / Dioxygen / Hydrocarbons
Function / homology
Function and homology information


phenol 2-monooxygenase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / monooxygenase activity / metal ion binding
Similarity search - Function
Phenol hydroxylase / Phenol hydroxylase / Phenol hydroxylase domain superfamily / Phenol hydroxylase conserved region / YHS domain / YHS domain / Methane/phenol monooxygenase, hydroxylase component / Propane/methane/phenol/toluene hydroxylase / Methane/Phenol/Alkene Hydroxylase / Ribonucleotide Reductase, subunit A ...Phenol hydroxylase / Phenol hydroxylase / Phenol hydroxylase domain superfamily / Phenol hydroxylase conserved region / YHS domain / YHS domain / Methane/phenol monooxygenase, hydroxylase component / Propane/methane/phenol/toluene hydroxylase / Methane/Phenol/Alkene Hydroxylase / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Ferritin-like superfamily / Ubiquitin-like (UB roll) / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / : / XENON / Phenol hydroxylase component PheO / Phenol hydroxylase component PheN / Phenol hydroxylase component PheL
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMcCormick, M.S. / Lippard, S.J.
Citation
Journal: Biochemistry / Year: 2011
Title: Analysis of Substrate Access to Active Sites in Bacterial Multicomponent Monooxygenase Hydroxylases: X-ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase from Pseudomonas sp. OX1.
Authors: McCormick, M.S. / Lippard, S.J.
#1: Journal: Biochemistry / Year: 2011
Title: Correction to Analysis of Substrate Access to Active Sites in Bacterial Multicomponent Monooxygenase Hydroxylases: X-ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase from Pseudomonas sp. OX1.
Authors: McCormick, M.S. / Lippard, S.J.
History
DepositionOct 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _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: Phenol hydroxylase component phN
B: Phenol hydroxylase component phN
C: Phenol hydroxylase component phL
D: Phenol hydroxylase component phL
E: Phenol hydroxylase component phO
F: Phenol hydroxylase component phO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,84950
Polymers223,8486
Non-polymers5,00144
Water10,593588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37390 Å2
ΔGint-216 kcal/mol
Surface area59090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.942, 141.761, 181.207
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Phenol hydroxylase component ... , 3 types, 6 molecules ABCDEF

#1: Protein Phenol hydroxylase component phN


Mass: 60217.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Alpha Subunit / Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Strain: OX1 / Gene: phN / Plasmid: pJSX148 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q84AQ2
#2: Protein Phenol hydroxylase component phL


Mass: 38458.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Beta Subunit / Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Strain: OX1 / Gene: phL / Plasmid: pJSX148 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q84AQ4
#3: Protein Phenol hydroxylase component phO


Mass: 13248.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Gamma Subunit / Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Strain: OX1 / Gene: phO / Plasmid: pJSX148 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q84AQ1

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Non-polymers , 8 types, 632 molecules

#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical...
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Xe
#9: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 588 / 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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Tris (pH 7.0), 150 mM Na2MoO4, 5% glycerol (v/v), 19% PEG 8000 (w/v), VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 24, 2006 / Details: Mirrors
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→38 Å / Num. all: 149674 / Num. obs: 138448 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.067
Reflection shellResolution: 1.95→2 Å / % possible all: 82.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
EPMRphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2INN

2inn


Resolution: 1.95→38 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.95 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22774 7356 5 %RANDOM
Rwork0.18295 ---
all0.18521 149674 --
obs0.18521 138448 92.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.577 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.95→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15331 0 120 588 16039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02215855
X-RAY DIFFRACTIONr_angle_refined_deg1.71.93621466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07551863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09724.179828
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.283152639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1751584
X-RAY DIFFRACTIONr_chiral_restr0.1360.22177
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212330
X-RAY DIFFRACTIONr_nbd_refined0.2150.27173
X-RAY DIFFRACTIONr_nbtor_refined0.3080.210820
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2767
X-RAY DIFFRACTIONr_metal_ion_refined0.0370.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.25
X-RAY DIFFRACTIONr_mcbond_it0.9311.59326
X-RAY DIFFRACTIONr_mcangle_it1.784214982
X-RAY DIFFRACTIONr_scbond_it3.15536985
X-RAY DIFFRACTIONr_scangle_it4.9564.56484
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 483 -
Rwork0.262 8964 -
obs--82.06 %

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