[English] 日本語
Yorodumi
- PDB-1diq: CRYSTAL STRUCTURE OF P-CRESOL METHYLHYDROXYLASE WITH SUBSTRATE BOUND -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1diq
TitleCRYSTAL STRUCTURE OF P-CRESOL METHYLHYDROXYLASE WITH SUBSTRATE BOUND
Components(P-CRESOL METHYLHYDROXYLASE4-Cresol dehydrogenase (hydroxylating)) x 2
KeywordsOXIDOREDUCTASE / FLAVOCYTOCHROME / ELECTRON-TRANSFER / FAD / HEME / P-CRESOL
Function / homology
Function and homology information


4-methylphenol dehydrogenase (hydroxylating) / 4-cresol dehydrogenase (hydroxylating) 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 / 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 / Cytochrome C oxidase, cbb3-type, subunit III / 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 / 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 / P-CRESOL / 4-cresol dehydrogenase [hydroxylating] cytochrome c subunit / 4-cresol dehydrogenase [hydroxylating] flavoprotein subunit
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.75 Å
AuthorsCunane, L.M. / Chen, Z.W. / Shamala, N. / Mathews, F.S. / Cronin, C.S. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)136,33112
Polymers133,2354
Non-polymers3,0958
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17570 Å2
ΔGint-170 kcal/mol
Surface area37660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.1, 130.5, 74.4
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAsymmetric unit contains flavoprotein dimer related by molecular 2-fold axis. Two cytochrome subunits located on periphery of flavoprotein dimer.

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein P-CRESOL METHYLHYDROXYLASE / 4-Cresol dehydrogenase (hydroxylating) / 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 / 4-Cresol dehydrogenase (hydroxylating) / 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

-
Non-polymers , 5 types, 350 molecules

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


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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-PCR / P-CRESOL / P-Cresol


Mass: 108.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8O
#6: Chemical ChemComp-HEC / HEME C / Heme C


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


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 7
Details: PEG 8000, Na/K phosphate, NaCl, Crystals soaked with substrate p-cresol , 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

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Mar 17, 1990
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→25 Å / Num. all: 35945 / Num. obs: 28932 / % possible obs: 80.5 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 47.4 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 16.5
Reflection shellResolution: 2.75→2.95 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.106 / % possible all: 65.5
Reflection shell
*PLUS
% possible obs: 65.5 %

-
Processing

Software
NameClassification
X-PLORmodel building
CNSrefinement
SDMSdata reduction
SDMSdata scaling
X-PLORphasing
RefinementResolution: 2.75→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.183 2909 -random
Rwork0.133 ---
all-35945 --
obs-28932 80.5 %-
Refinement stepCycle: LAST / Resolution: 2.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9178 0 210 342 9730
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.78
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.8
LS refinement shell
*PLUS
Highest resolution: 2.75 Å / Lowest resolution: 3 Å / Rfactor Rfree: 0.289 / Rfactor Rwork: 0.21

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more