[English] 日本語
Yorodumi
- PDB-1ahv: STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE I... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ahv
TitleSTRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE IN COMPLEX WITH 2-NITRO-P-CRESOL
ComponentsVANILLYL-ALCOHOL OXIDASE
KeywordsFLAVOENZYME / OXIDASE / CATALYSIS
Function / homology
Function and homology information


vanillyl-alcohol oxidase / vanillyl-alcohol oxidase activity / methanol metabolic process / FAD binding / peroxisome
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
FLAVIN-ADENINE DINUCLEOTIDE / 2-NITRO-P-CRESOL / Vanillyl-alcohol oxidase
Similarity search - Component
Biological speciesPenicillium simplicissimum (fungus)
MethodX-RAY DIFFRACTION / DENSITY AVERAGING, LEAST SQUARES REFINEMENT / Resolution: 3.1 Å
AuthorsMattevi, A.
CitationJournal: Structure / Year: 1997
Title: Crystal structures and inhibitor binding in the octameric flavoenzyme vanillyl-alcohol oxidase: the shape of the active-site cavity controls substrate specificity.
Authors: Mattevi, A. / Fraaije, M.W. / Mozzarelli, A. / Olivi, L. / Coda, A. / van Berkel, W.J.
History
DepositionApr 10, 1997-
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VANILLYL-ALCOHOL OXIDASE
B: VANILLYL-ALCOHOL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,0926
Polymers126,2142
Non-polymers1,8774
Water0
1
A: VANILLYL-ALCOHOL OXIDASE
B: VANILLYL-ALCOHOL OXIDASE
hetero molecules

A: VANILLYL-ALCOHOL OXIDASE
B: VANILLYL-ALCOHOL OXIDASE
hetero molecules

A: VANILLYL-ALCOHOL OXIDASE
B: VANILLYL-ALCOHOL OXIDASE
hetero molecules

A: VANILLYL-ALCOHOL OXIDASE
B: VANILLYL-ALCOHOL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)512,36624
Polymers504,8578
Non-polymers7,50916
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11570 Å2
ΔGint-68 kcal/mol
Surface area36710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.620, 140.620, 132.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.30275, -0.95253, 0.03221), (-0.95246, -0.3036, -0.02565), (0.03421, -0.02292, -0.99915)
Vector: 114.26009, 159.96399, 108.75453)

-
Components

#1: Protein VANILLYL-ALCOHOL OXIDASE /


Mass: 63107.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: FUNGUS / Source: (natural) Penicillium simplicissimum (fungus) / Cellular location: INTRACELLULARGlossary of biology / Organelle: PEROXISOMESPeroxisome / References: UniProt: P56216, alcohol oxidase
#2: 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
#3: Chemical ChemComp-NCR / 2-NITRO-P-CRESOL


Mass: 153.135 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO3

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 40 % / Description: BINDING STUDIES
Crystal growpH: 4.6 / Details: FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 %(w/v)PEG40001reservoir
20.1 Msodium acetate/HCl1reservoir
31
41
51
61
71
81

-
Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 21522 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.62 / Net I/σ(I): 8
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 3 / Rsym value: 0.274 / % possible all: 90.1
Reflection
*PLUS
Num. measured all: 43741 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 90.1 %

-
Processing

Software
NameVersionClassification
CCP4model building
TNT5Erefinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: DENSITY AVERAGING, LEAST SQUARES REFINEMENT
Resolution: 3.1→30 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rfree0.24 1000 4 %
Rwork0.205 --
all0.206 21522 -
obs0.206 21522 94.3 %
Solvent computationSolvent model: BABINET
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8782 0 128 0 8910
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.006916030
X-RAY DIFFRACTIONt_angle_deg2.21239815
X-RAY DIFFRACTIONt_dihedral_angle_d17.55296180
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.006216100
X-RAY DIFFRACTIONt_gen_planes0.0051312250
X-RAY DIFFRACTIONt_it8.4915665
X-RAY DIFFRACTIONt_nbd0.026286125
Software
*PLUS
Name: TNT / Version: 5-E / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.249 / Lowest resolution: 100 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.006100
X-RAY DIFFRACTIONt_plane_restr0.005250
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.5180

+
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