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- PDB-2inn: Structure of the Phenol Hydroxyalse-Regulatory Protein Complex -

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Basic information

Entry
Database: PDB / ID: 2inn
TitleStructure of the Phenol Hydroxyalse-Regulatory Protein Complex
Components(Phenol hydroxylase component ...) x 4
KeywordsOXIDOREDUCTASE / hydroxylase / four-helix bundle / diiron / phenol / complex
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 / oxidoreductase activity / metal ion binding
Similarity search - Function
Phenol hydroxylase / Phenol hydroxylase / Phenol hydroxylase domain superfamily / Phenol hydroxylase conserved region / YHS domain / YHS domain / Monooxygenase component MmoB/DmpM / Phenol Hydroxylase P2 Protein / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily ...Phenol hydroxylase / Phenol hydroxylase / Phenol hydroxylase domain superfamily / Phenol hydroxylase conserved region / YHS domain / YHS domain / Monooxygenase component MmoB/DmpM / Phenol Hydroxylase P2 Protein / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / 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 / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / MOLYBDATE ION / Phenol hydroxylase component PheO / Phenol hydroxylase component PheN / Phenol hydroxylase component PheM / Phenol hydroxylase component PheL
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsSazinsky, M.H. / Dunten, P.W. / McCormick, M.S. / Lippard, S.J.
CitationJournal: Biochemistry / Year: 2006
Title: X-ray Structure of a Hydroxylase-Regulatory Protein Complex from a Hydrocarbon-Oxidizing Multicomponent Monooxygenase, Pseudomonas sp. OX1 Phenol Hydroxylase.
Authors: Sazinsky, M.H. / Dunten, P.W. / McCormick, M.S. / Didonato, A. / Lippard, S.J.
History
DepositionOct 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
L: Phenol hydroxylase component phM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,87814
Polymers238,3647
Non-polymers5147
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32270 Å2
ΔGint-191 kcal/mol
Surface area61910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.453, 146.925, 189.787
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is an alpha, beta, gamma heterodimer complexed to one molecule of the regulatory protein. The molecule in asymmetric unit is the biologically relavent asembly.

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Components

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Phenol hydroxylase component ... , 4 types, 7 molecules ABCDEFL

#1: Protein Phenol hydroxylase component phN


Mass: 61058.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: phN / Production host: Escherichia coli (E. coli) / References: UniProt: Q84AQ2
#2: Protein Phenol hydroxylase component phL


Mass: 39255.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: phL / Production host: Escherichia coli (E. coli) / References: UniProt: Q84AQ4
#3: Protein Phenol hydroxylase component phO


Mass: 13482.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: phO / Production host: Escherichia coli (E. coli) / References: UniProt: Q84AQ1
#4: Protein Phenol hydroxylase component phM


Mass: 10770.048 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: phM / Production host: Escherichia coli (E. coli) / References: UniProt: Q84AQ3

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Non-polymers , 4 types, 311 molecules

#5: Chemical
ChemComp-FE / FE (III) ION / Iron


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE / Molybdate


Mass: 159.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: MoO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Tris, pH 7.0, 150 mM Na2MoO4, 5% glycerol, and 17-20% PEG 8000 (w/w), VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 68087 / % possible obs: 85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 17.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5 / Num. unique all: 2565 / Rsym value: 0.26 / % possible all: 54

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.89 / SU B: 11.992 / SU ML: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2973 5.1 %RANDOM
Rwork0.202 ---
all0.213 68087 --
obs0.206 58555 86.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.988 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20 Å2
2---0.76 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16074 0 11 304 16389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.02216542
X-RAY DIFFRACTIONr_angle_refined_deg2.6291.93122420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.99251955
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64624.276877
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.042152772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9841589
X-RAY DIFFRACTIONr_chiral_restr0.170.22286
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212942
X-RAY DIFFRACTIONr_nbd_refined0.2910.28830
X-RAY DIFFRACTIONr_nbtor_refined0.3430.211040
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2856
X-RAY DIFFRACTIONr_metal_ion_refined0.1630.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0390.23
X-RAY DIFFRACTIONr_mcbond_it1.5221.510072
X-RAY DIFFRACTIONr_mcangle_it2.098215717
X-RAY DIFFRACTIONr_scbond_it3.54137643
X-RAY DIFFRACTIONr_scangle_it5.14.56703
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 137 -
Rwork0.24 2565 -
obs-2702 54.8 %

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