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- PDB-1dii: CRYSTAL STRUCTURE OF P-CRESOL METHYLHYDROXYLASE AT 2.5 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1dii
TitleCRYSTAL STRUCTURE OF P-CRESOL METHYLHYDROXYLASE AT 2.5 A RESOLUTION
Components(P-CRESOL METHYLHYDROXYLASE) x 2
KeywordsOXIDOREDUCTASE / FLAVOCYTOCHROME / ELECTRON-TRANSFER / FAD / HEME
Function / homology
Function and homology information


4-methylphenol dehydrogenase (hydroxylating) / 4-cresol dehydrogenase (hydroxylating) activity / lactate catabolic process / D-lactate dehydrogenase (cytochrome) activity / 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
FLAVIN-ADENINE DINUCLEOTIDE / HEME C / 4-cresol dehydrogenase [hydroxylating] cytochrome c subunit / 4-cresol dehydrogenase [hydroxylating] flavoprotein subunit
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsCunane, L.M. / Chen, Z.W. / Shamala, N. / Mathews, F.S. / Cronin, C.N. / McIntire, W.S.
Citation
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.
#1: Journal: Biochemistry / Year: 1991
Title: Three-dimensional Structure of p-Cresol Methylhydroxylase (Flavocytochrome c) from Pseudomonas putida at 3.0 A Resolution
Authors: Mathews, F.S. / Chen, Z.W. / Bellamy, H. / McIntire, W.S.
History
DepositionNov 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _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_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P-CRESOL METHYLHYDROXYLASE
C: P-CRESOL METHYLHYDROXYLASE
B: P-CRESOL METHYLHYDROXYLASE
D: P-CRESOL METHYLHYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,11410
Polymers133,2354
Non-polymers2,8796
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16750 Å2
ΔGint-165 kcal/mol
Surface area38320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.3, 130.6, 74.1
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsASYMMETRIC UNIT CONTAINS A FLAVOPROTEIN DIMER RELATED BY A MOLECULAR 2-FOLD AXIS. TWO CYTOCHROME SUBUNITS ARE BOUND ON THE PERIPHERY OF THE FLAVOPROTEIN DIMER.

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein P-CRESOL METHYLHYDROXYLASE / PCMH


Mass: 58005.965 Da / Num. of mol.: 2 / Fragment: FLAVOPROTEIN SUBUNIT / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / Cellular location: PERIPLASM / Strain: NCIMB 9869 / References: UniProt: P09788, EC: 1.17.99.1
#2: Protein P-CRESOL METHYLHYDROXYLASE / PCMH


Mass: 8611.642 Da / Num. of mol.: 2 / Fragment: CYTOCHROME SUBUNIT / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / Cellular location: PERIPLASM / Strain: NCIMB 9869 / References: UniProt: P09787, EC: 1.17.99.1

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Non-polymers , 4 types, 391 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-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 7
Details: PEG 8000, NA/K PHOSPHATE, NACL, pH 7.0, LIQUID DIFFUSION, temperature 298K
Crystal
*PLUS
Density % sol: 58 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: or interface diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
28 %PEG80001reservoir
350 mMphosphate1reservoir
40.1 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: May 31, 1990
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 47875 / Num. obs: 42484 / % possible obs: 89.5 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 41.8 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 8.3
Reflection shellResolution: 2.5→2.7 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.224 / % possible all: 87
Reflection shell
*PLUS
% possible obs: 87 %

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Processing

Software
NameClassification
X-PLORmodel building
CNSrefinement
SDMSdata reduction
SDMSdata scaling
X-PLORphasing
RefinementResolution: 2.5→30 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.23 4282 -RANDOM
Rwork0.172 ---
obs0.172 42435 88.4 %-
all-47875 --
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9226 0 194 385 9805
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.74
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_deg1.8
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.86 Å / Rfactor Rfree: 0.331 / Rfactor Rwork: 0.287

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