[English] 日本語
Yorodumi
- PDB-3sx1: Hansenula polymorpha copper amine oxidase-1 in its apo form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sx1
TitleHansenula polymorpha copper amine oxidase-1 in its apo form
ComponentsPeroxisomal primary amine oxidase
KeywordsOXIDOREDUCTASE / peroxisome
Function / homology
Function and homology information


: / : / : / primary-amine oxidase / amine metabolic process / quinone binding / peroxisome / copper ion binding
Similarity search - Function
Copper amine oxidase, N3-terminal / Copper amine oxidase, N2-terminal / Copper amine oxidase, N2 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, N3-terminal / Copper amine oxidase, N2-terminal / Copper amine oxidase, N2 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
PHOSPHATE ION / Peroxisomal primary amine oxidase
Similarity search - Component
Biological speciesPichia angusta (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsKlema, V.J. / Johnson, B.J. / Wilmot, C.M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: The precursor form of Hansenula polymorpha copper amine oxidase 1 in complex with CuI and CoII.
Authors: Klema, V.J. / Johnson, B.J. / Klinman, J.P. / Wilmot, C.M.
History
DepositionJul 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Sep 13, 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 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Peroxisomal primary amine oxidase
B: Peroxisomal primary amine oxidase
C: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,28218
Polymers232,8983
Non-polymers1,38415
Water46,5512584
1
A: Peroxisomal primary amine oxidase
hetero molecules

A: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,37014
Polymers155,2652
Non-polymers1,10512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area13760 Å2
ΔGint-58 kcal/mol
Surface area44130 Å2
MethodPISA
2
B: Peroxisomal primary amine oxidase
C: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,09711
Polymers155,2652
Non-polymers8329
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13680 Å2
ΔGint-63 kcal/mol
Surface area44680 Å2
MethodPISA
3
A: Peroxisomal primary amine oxidase
hetero molecules

A: Peroxisomal primary amine oxidase
hetero molecules

B: Peroxisomal primary amine oxidase
C: Peroxisomal primary amine oxidase
hetero molecules

B: Peroxisomal primary amine oxidase
C: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)468,56436
Polymers465,7966
Non-polymers2,76930
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation5_445x-1/2,y-1/2,z1
crystal symmetry operation7_445-x-1/2,y-1/2,-z+1/21
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area47020 Å2
ΔGint-221 kcal/mol
Surface area127600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.617, 153.636, 223.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-912-

HOH

21B-1183-

HOH

31B-1521-

HOH

-
Components

#1: Protein Peroxisomal primary amine oxidase / Copper amine oxidase / Methylamine oxidase


Mass: 77632.617 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pichia angusta (fungus) / Gene: AMO / Production host: Escherichia coli (E. coli) / References: UniProt: P12807, primary-amine oxidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2584 / 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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 8% PEG 8000, 0.28 M potassium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. all: 247478 / Num. obs: 240796 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10 % / Rsym value: 0.074 / Net I/σ(I): 32.3
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.447 / % possible all: 88.1

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2OOV

2oov


Resolution: 1.73→31.61 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.133 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1628 12085 5 %RANDOM
Rwork0.13205 ---
obs0.13359 228647 97.4 %-
all-234751 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.719 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.73→31.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15596 0 89 2584 18269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02216499
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.95822533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.80652096
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49823.789768
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.738152669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.51215101
X-RAY DIFFRACTIONr_chiral_restr0.1470.22401
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02112855
X-RAY DIFFRACTIONr_mcbond_it1.5271.510065
X-RAY DIFFRACTIONr_mcangle_it2.493216424
X-RAY DIFFRACTIONr_scbond_it3.94936434
X-RAY DIFFRACTIONr_scangle_it6.1384.56044
LS refinement shellResolution: 1.732→1.777 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 869 -
Rwork0.202 15773 -
obs--92.1 %
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)
10.0290.0015-0.02510.0112-0.00470.1016-0.01760.00510.0004-0.00050.003-0.00180.0359-0.00430.01450.0167-0.00420.00620.0055-0.00460.0094-1.1887-3.399138.2791
20.0182-0.0145-0.02060.06810.02830.08170.0125-0.00380.0003-0.0217-0.0073-0.0031-0.027-0.0113-0.00520.01340.00190.00320.0060.0010.0053-68.6292-5.874228.8479
30.02230.01410.00610.1540.03780.0225-0.0009-0.0027-0.0081-0.03950.0054-0.025-0.0118-0.0008-0.00460.0127-0.00510.00660.0085-0.00320.0072-54.5924-35.0915.2378
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 672
2X-RAY DIFFRACTION1A693 - 698
3X-RAY DIFFRACTION1A699 - 3000
4X-RAY DIFFRACTION2B16 - 672
5X-RAY DIFFRACTION2B693 - 697
6X-RAY DIFFRACTION2B698 - 3003
7X-RAY DIFFRACTION3C16 - 671
8X-RAY DIFFRACTION3C693 - 696
9X-RAY DIFFRACTION3C697 - 3004

+
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