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- PDB-2inp: Structure of the Phenol Hydroxylase-Regulatory Protein Complex -

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Basic information

Entry
Database: PDB / ID: 2inp
TitleStructure of the Phenol Hydroxylase-Regulatory Protein Complex
Components(Phenol hydroxylase component ...) x 4
KeywordsOXIDOREDUCTASE / hydroxylase / diiron / four-helix bundle / regulatory protein
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 / 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
: / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSazinsky, M.S. / 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 1.3Aug 30, 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_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.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_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_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_conn.ptnr2_label_seq_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
L: Phenol hydroxylase component phM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,81713
Polymers229,4637
Non-polymers3546
Water18,4111022
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31760 Å2
ΔGint-197 kcal/mol
Surface area61950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.751, 146.305, 190.020
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 ... , 4 types, 7 molecules ABCDEFL

#1: Protein Phenol hydroxylase component phN


Mass: 58401.516 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: 37968.840 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: 13116.934 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: 10488.678 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 , 3 types, 1028 molecules

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


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1022 / 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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 293 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 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 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: 2.3→30 Å / Num. all: 108695 / Num. obs: 108695 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.089 / Rsym value: 0.088 / Net I/σ(I): 16.5
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 4.9 / Num. unique all: 7777 / Rsym value: 0.448 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2INN

2inn


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.519 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.281 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.236 5424 5 %RANDOM
Rwork0.192 ---
all0.201 110224 --
obs0.198 108608 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.83 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å20 Å20 Å2
2---1.67 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15994 0 6 1022 17022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02216454
X-RAY DIFFRACTIONr_angle_refined_deg2.0271.9322303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg751951
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49524.266865
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.067152738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.141586
X-RAY DIFFRACTIONr_chiral_restr0.150.22278
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212863
X-RAY DIFFRACTIONr_nbd_refined0.2310.28053
X-RAY DIFFRACTIONr_nbtor_refined0.3130.210933
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.21149
X-RAY DIFFRACTIONr_metal_ion_refined0.0340.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3150.210
X-RAY DIFFRACTIONr_mcbond_it1.2351.510098
X-RAY DIFFRACTIONr_mcangle_it1.944215667
X-RAY DIFFRACTIONr_scbond_it3.2237560
X-RAY DIFFRACTIONr_scangle_it4.6974.56636
LS refinement shellResolution: 2.302→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 388 -
Rwork0.233 7389 -
obs-7777 98.57 %

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