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- PDB-1foh: PHENOL HYDROXYLASE FROM TRICHOSPORON CUTANEUM -

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Basic information

Entry
Database: PDB / ID: 1foh
TitlePHENOL HYDROXYLASE FROM TRICHOSPORON CUTANEUM
ComponentsPHENOL HYDROXYLASE
KeywordsFLAVIN / PHENOL HYDROXYLASE / MONOOXYGENASE / OXIDOREDUCTASE
Function / homology
Function and homology information


phenol-containing compound catabolic process / phenol 2-monooxygenase (NADPH) / phenol 2-monooxygenase activity / FAD binding
Similarity search - Function
Phenol hydroxylase, C-terminal dimerisation domain / Phenol hydroxylase, C-terminal dimerisation domain / Phenol hydroxylase, C-terminal TRX-fold domain superfamily / Phenol hydroxylase, C-terminal dimerisation domain / : / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain ...Phenol hydroxylase, C-terminal dimerisation domain / Phenol hydroxylase, C-terminal dimerisation domain / Phenol hydroxylase, C-terminal TRX-fold domain superfamily / Phenol hydroxylase, C-terminal dimerisation domain / : / D-Amino Acid Oxidase, subunit A, domain 2 / 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 / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PHENOL / Phenol hydroxylase
Similarity search - Component
Biological speciesTrichosporon cutaneum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsEnroth, C. / Neujahr, H. / Schneider, G. / Lindqvist, Y.
Citation
Journal: Structure / Year: 1998
Title: The crystal structure of phenol hydroxylase in complex with FAD and phenol provides evidence for a concerted conformational change in the enzyme and its cofactor during catalysis.
Authors: Enroth, C. / Neujahr, H. / Schneider, G. / Lindqvist, Y.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Analysis of Phenol Hydroxylase from Trichosporon Cutaneum
Authors: Enroth, C. / Huang, W. / Waters, S. / Neujahr, H. / Lindqvist, Y. / Schneider, G.
History
DepositionMar 26, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _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
B: PHENOL HYDROXYLASE
C: PHENOL HYDROXYLASE
D: PHENOL HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,30912
Polymers300,7914
Non-polymers3,5198
Water21,4201189
1
A: PHENOL HYDROXYLASE
C: PHENOL HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,1556
Polymers150,3952
Non-polymers1,7594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-12 kcal/mol
Surface area47210 Å2
MethodPISA
2
B: PHENOL HYDROXYLASE
D: PHENOL HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,1556
Polymers150,3952
Non-polymers1,7594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-11 kcal/mol
Surface area47180 Å2
MethodPISA
3
A: PHENOL HYDROXYLASE
C: PHENOL HYDROXYLASE
hetero molecules

B: PHENOL HYDROXYLASE
D: PHENOL HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,30912
Polymers300,7914
Non-polymers3,5198
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_746-x+2,y-1/2,-z+11
Buried area15740 Å2
ΔGint-25 kcal/mol
Surface area93180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.030, 150.680, 114.920
Angle α, β, γ (deg.)90.00, 114.68, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.767711, -0.126133, -0.628259), (-0.131725, -0.990561, 0.037908), (-0.627111, 0.053655, -0.77708)83.14092, 125.31898, 166.83136
2given(-0.516787, 0.103477, 0.849837), (0.151036, -0.966079, 0.209476), (0.842686, 0.23661, 0.483628)26.02597, 98.03886, -28.85406
3given(-0.942812, 0.090767, 0.320728), (-0.018173, 0.946782, -0.321363), (-0.332829, -0.308814, -0.890988)106.83795, 23.09471, 179.24576

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Components

#1: Protein
PHENOL HYDROXYLASE


Mass: 75197.641 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichosporon cutaneum (fungus) / Cell line: 293 / Gene: PHYA / Plasmid: PRJ6C / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P15245, phenol 2-monooxygenase (NADPH)
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1189 / 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: 2.5 Å3/Da / Density % sol: 47.3 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlenzyme1drop
220 mMphenol1drop
3120 mMTris-HCl1reservoiror 0.21M KCl and 16% PEG4000
40.52 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.9997
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9997 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 118897 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 35.5 Å2 / Rsym value: 0.095 / Net I/σ(I): 7.8
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.335 / % possible all: 94.1
Reflection
*PLUS
Rmerge(I) obs: 0.095
Reflection shell
*PLUS
% possible obs: 94.1 % / Rmerge(I) obs: 0.335

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.4→12 Å / Cross valid method: R FREE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.278 3263 3 %RANDOM
Rwork0.217 ---
obs-118539 98 %-
Displacement parametersBiso mean: 41.1 Å2
Refine analyzeLuzzati d res low obs: 12 Å
Refinement stepCycle: LAST / Resolution: 2.4→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20806 0 240 1189 22235
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.022
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS

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