[English] 日本語
Yorodumi
- PDB-1sii: AGAO in covalent complex with the inhibitor NOBA ("4-(2-naphthylo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sii
TitleAGAO in covalent complex with the inhibitor NOBA ("4-(2-naphthyloxy)-2-butyn-1-amine")
ComponentsPhenylethylamine oxidase
KeywordsOXIDOREDUCTASE / CAO / CuAO / COPPER-CONTAINING / AMINE OXIDASE / TPQ / QUINONE / TRIHYDROXYPHENYLALANINE QUINONE / NOBA / 4-(2-naphthyloxy)-2-butyn-1-amine / 4-(aryloxy)-2-butynamine / suicide inhibition
Function / homology
Function and homology information


: / : / : / primary-amine oxidase / amine metabolic process / quinone binding / copper ion binding
Similarity search - Function
Copper amine oxidase, N3 domain / Copper amine oxidase, catalytic domain / Copper amine oxidase copper-binding site signature. / Copper amine oxidase topaquinone signature. / Nuclear Transport Factor 2; Chain: A, - #40 / Copper amine oxidase / Copper amine oxidase, catalytic domain / Copper amine oxidase, N-terminal / Copper amine oxidase, catalytic domain superfamily / Copper amine oxidase, enzyme domain ...Copper amine oxidase, N3 domain / Copper amine oxidase, catalytic domain / Copper amine oxidase copper-binding site signature. / Copper amine oxidase topaquinone signature. / Nuclear Transport Factor 2; Chain: A, - #40 / Copper amine oxidase / Copper amine oxidase, catalytic domain / Copper amine oxidase, N-terminal / Copper amine oxidase, catalytic domain superfamily / Copper amine oxidase, enzyme domain / Beta-galactosidase; Chain A, domain 5 / Nuclear Transport Factor 2; Chain: A, / Distorted Sandwich / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Phenylethylamine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGuss, J.M. / Langley, D.B. / Duff, A.P.
CitationJournal: Biochemistry / Year: 2004
Title: Differential Inhibition of Six Copper Amine Oxidases by a Family of 4-(Aryloxy)-2-butynamines: Evidence for a New Mode of Inactivation.
Authors: O'Connell, K.M. / Langley, D.B. / Shepard, E.M. / Duff, A.P. / Jeon, H.B. / Sun, G. / Freeman, H.C. / Guss, J.M. / Sayre, L.M. / Dooley, D.M.
History
DepositionFeb 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 10, 2011Group: Atomic model / Database references / Other
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3426
Polymers71,9751
Non-polymers3675
Water8,917495
1
A: Phenylethylamine oxidase
hetero molecules

A: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,68412
Polymers143,9502
Non-polymers73410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area15280 Å2
ΔGint-107 kcal/mol
Surface area40750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)158.060, 62.619, 91.990
Angle α, β, γ (deg.)90.00, 112.11, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe asymmetric unit contains half of one biological unit. Crystallographic symmetry is required to generate the other half of the dimer.

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Phenylethylamine oxidase / Amine oxidase


Mass: 71975.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Arthrobacter globiformis copper amine oxidase (AGAO) with modified amino acid 382 TPQ - 4-(2-naphthyloxy)-2-butyn-1-amine moiety
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Gene: ATCC8010, IFO12137 / Plasmid: PAGAO2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P46881, EC: 1.4.3.6

-
Non-polymers , 5 types, 500 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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.: 495 / 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: 3.05 Å3/Da / Density % sol: 59.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 4 microlitres of (AGAO 10 mg/ml, 50mM HEPES pH 7.0, 5-fold molar excess of NOBA, incubated at RT for four hours) plus 4 microlitres of the reservoir solution (1.5M (NH4)2SO4, 260micromolar ...Details: 4 microlitres of (AGAO 10 mg/ml, 50mM HEPES pH 7.0, 5-fold molar excess of NOBA, incubated at RT for four hours) plus 4 microlitres of the reservoir solution (1.5M (NH4)2SO4, 260micromolar CuSO4, 100mM MES pH 6.5). Crystals cryoprotected by gradual, successive transfers over 2 hours, finally to a solution of 1.5M (NH4)2SO4, 100mM MES pH 6.5, 2.5mM EGTA, 30% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.7→19.88 Å / Num. all: 85823 / Num. obs: 85823 / Observed criterion σ(I): -3 / Redundancy: 10 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 13
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.3 / % possible all: 76.4

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.88 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.82 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: overall anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18275 4333 5 %RANDOM
Rwork0.15727 ---
obs0.15858 81489 93.37 %-
all-85822 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.482 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å20.22 Å2
2--2.11 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4884 0 19 495 5398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215053
X-RAY DIFFRACTIONr_bond_other_d0.0020.024539
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9476884
X-RAY DIFFRACTIONr_angle_other_deg0.796310501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3665619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2749
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025712
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021097
X-RAY DIFFRACTIONr_nbd_refined0.1940.2839
X-RAY DIFFRACTIONr_nbd_other0.250.25438
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.23063
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2388
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0180.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3060.2198
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it3.1423087
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.45935001
X-RAY DIFFRACTIONr_scbond_it6.3441966
X-RAY DIFFRACTIONr_scangle_it8.47161883
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.742 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 323
Rwork0.241 5635
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.45930.32620.27340.28240.0188-0.12950.0814-0.1313-0.0139-0.0307-0.0716-0.0716-0.02310.1358-0.00970.0185-0.0483-0.00450.138-0.00320.080422.28434.698443.2182
20.26780.0464-0.2118-0.0356-0.19520.69960.00180.08050.0116-0.02490.0139-0.00190.03390.1631-0.01570.08210.0180.00950.0894-0.00150.04279.0076-2.795214.2145
3-0.8017-0.1262-0.68630.6259-0.698-0.46550.13880.08380.1418-0.04360.0673-0.0348-0.12020.1775-0.20610.07380.00860.02290.07520.01060.0835-15.532321.311728.9919
40.3093-0.0119-0.22150.0286-0.05070.44810.016-0.04960.0318-0.004-0.0060.00010.01690.1062-0.00990.065-0.0048-0.01150.0389-0.00610.0695-5.0779-0.447145.3268
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 997 - 97
2X-RAY DIFFRACTION2AA100 - 20398 - 201
3X-RAY DIFFRACTION3AA204 - 229202 - 227
4X-RAY DIFFRACTION4AA230 - 628228 - 626

+
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