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

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Basic information

Entry
Database: PDB / ID: 1wve
Titlep-Cresol Methylhydroxylase: Alteration of the Structure of the Flavoprotein Subunit upon its Binding to the Cytochrome Subunit
Components(4-cresol dehydrogenase [hydroxylating] ...) x 2
KeywordsOXIDOREDUCTASE / FLAVOCYTOCHROME / ELECTRON-TRANSFER / FAD / HEME
Function / homology
Function and homology information


4-methylphenol dehydrogenase (hydroxylating) / 4-cresol dehydrogenase (hydroxylating) activity / D-lactate dehydrogenase (cytochrome) activity / lactate catabolic process / D-lactate dehydrogenase (NAD+) activity / FAD binding / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Vanillyl-alcohol Oxidase; Chain A, domain 4 / Vanillyl-alcohol Oxidase; Chain A, domain 4 / FAD-linked oxidases, C-terminal domain / FAD-linked oxidase, C-terminal / Cytokinin dehydrogenase, C-terminal domain superfamily / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / Vanillyl-alcohol Oxidase; Chain A, domain 3 / FAD-linked oxidase-like, C-terminal / 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 / FAD-linked oxidase, C-terminal / Cytokinin dehydrogenase, C-terminal domain superfamily / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / Vanillyl-alcohol Oxidase; Chain A, domain 3 / FAD-linked oxidase-like, C-terminal / 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 / Cytochrome C oxidase, cbb3-type, subunit III / 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 / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / 4-cresol dehydrogenase [hydroxylating] cytochrome c subunit / 4-cresol dehydrogenase [hydroxylating] flavoprotein subunit
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 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: 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: 4-cresol dehydrogenase [hydroxylating] cytochrome c subunit
B: 4-cresol dehydrogenase [hydroxylating] flavoprotein subunit
D: 4-cresol dehydrogenase [hydroxylating] cytochrome c subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,57718
Polymers132,9734
Non-polymers3,60414
Water19,8711103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17510 Å2
ΔGint-145 kcal/mol
Surface area37050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.830, 118.600, 136.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a heterotetramer.

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Components

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4-cresol dehydrogenase [hydroxylating] ... , 2 types, 4 molecules ABCD

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


Mass: 57874.770 Da / Num. of mol.: 2
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
#2: Protein 4-cresol dehydrogenase [hydroxylating] cytochrome c subunit / Flavocytochrome c / P-cresol methylhydroxylase cytochrome subunit


Mass: 8611.642 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P09787, EC: 1.17.99.1

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Non-polymers , 6 types, 1117 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#7: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1103 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 8000, Tris, ammonium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 3, 1998
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 103498 / Num. obs: 94080 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.6
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 2.1 / % possible all: 52.3

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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: 1.85→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.194 9407 -RANDOM
Rwork0.159 ---
all-102608 --
obs-94068 91.7 %-
Displacement parametersBiso mean: 22.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9347 0 226 1119 10692
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d1.06
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.85-1.960.302510540.2813X-RAY DIFFRACTION93826
1.96-2.120.230615240.2043X-RAY DIFFRACTION139926
2.12-2.330.199316090.1614X-RAY DIFFRACTION150966
2.33-2.670.189917050.1478X-RAY DIFFRACTION152546
2.67-3.360.191917630.1495X-RAY DIFFRACTION153746
3.36-28.470.170117520.143X-RAY DIFFRACTION155636

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