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- PDB-1wvf: p-Cresol Methylhydroxylase: Alteration of the Structure of the Fl... -

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Basic information

Entry
Database: PDB / ID: 1wvf
Titlep-Cresol Methylhydroxylase: Alteration of the Structure of the Flavoprotein Subunit upon its Binding to the Cytochrome Subunit
Components4-cresol dehydrogenase [hydroxylating] flavoprotein subunit
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / ELECTRON-TRANSFER / FAD
Function / homology
Function and homology information


4-methylphenol dehydrogenase (hydroxylating) / 4-cresol dehydrogenase (hydroxylating) activity / FAD binding
Similarity search - Function
Vanillyl-alcohol Oxidase; Chain A, domain 4 / Vanillyl-alcohol Oxidase; Chain A, domain 4 / FAD-linked oxidases, C-terminal domain / Cytokinin dehydrogenase, C-terminal domain superfamily / FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 ...Vanillyl-alcohol Oxidase; Chain A, domain 4 / Vanillyl-alcohol Oxidase; Chain A, domain 4 / FAD-linked oxidases, C-terminal domain / Cytokinin dehydrogenase, C-terminal domain superfamily / FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / Vanillyl-alcohol Oxidase; Chain A, domain 3 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / 4-cresol dehydrogenase [hydroxylating] flavoprotein subunit
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsCunane, L.M. / Chen, Z.-W. / McIntire, W.S. / Mathews, F.S.
Citation
Journal: Biochemistry / Year: 2005
Title: p-Cresol Methylhydroxylase: Alteration of the Structure of the Flavoprotein Subunit upon Its Binding to the Cytochrome Subunit
Authors: Cunane, L.M. / Chen, Z.-W. / McIntire, W.S. / Mathews, F.S.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Structures of the flavocytochrome p-cresol methylhydroxylase and its enzyme-substrate complex: gated substrate entry and proton relays support the proposed catalytic mechanism
Authors: Cunane, L.M. / Chen, Z.-W. / Shamala, N. / Mathews, F.S. / Cronin, C.N. / McIntire, W.S.
History
DepositionDec 15, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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: 4-cresol dehydrogenase [hydroxylating] flavoprotein subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0007
Polymers57,8751
Non-polymers1,1256
Water14,430801
1
A: 4-cresol dehydrogenase [hydroxylating] flavoprotein subunit
hetero molecules

A: 4-cresol dehydrogenase [hydroxylating] flavoprotein subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,00014
Polymers115,7502
Non-polymers2,25112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11090 Å2
ΔGint-92 kcal/mol
Surface area32600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)88.640, 116.910, 50.220
Angle α, β, γ (deg.)90.00, 113.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2242-

HOH

21A-2376-

HOH

31A-2467-

HOH

41A-2468-

HOH

51A-2471-

HOH

DetailsThe biological assembly is a homodimer.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 4-cresol dehydrogenase [hydroxylating] flavoprotein subunit / P-cresol methylhydroxylase / PCMH


Mass: 57874.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P09788, EC: 1.17.99.1

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Non-polymers , 5 types, 807 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: 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
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 801 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: PEG 1500, acetate, magnesium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: SBC / Detector: CCD / Date: Jun 27, 1999
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. all: 115051 / Num. obs: 100440 / % possible obs: 87.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 19.6
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 4.1 / % possible all: 46.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1DII

1dii


Resolution: 1.3→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.167 10064 -RANDOM
Rwork0.146 ---
all-115001 --
obs-100433 87.3 %-
Displacement parametersBiso mean: 13.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.13 Å0.11 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4025 0 74 801 4900
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.63
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d1.28
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.3-1.380.2189850.1945X-RAY DIFFRACTION85846
1.38-1.490.198214870.1757X-RAY DIFFRACTION136116
1.49-1.640.176618180.1547X-RAY DIFFRACTION167046
1.64-1.870.172818650.1456X-RAY DIFFRACTION169676
1.87-2.360.162919730.1466X-RAY DIFFRACTION171386
2.36-36.230.161419360.1423X-RAY DIFFRACTION173656

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