[English] 日本語
Yorodumi
- PDB-3sxx: Hansenula polymorpha copper amine oxidase-1 in complex with Co(II) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sxx
TitleHansenula polymorpha copper amine oxidase-1 in complex with Co(II)
ComponentsPeroxisomal primary amine oxidase
KeywordsOXIDOREDUCTASE / peroxisome
Function / homology
Function and homology information


primary-amine oxidase / primary methylamine oxidase activity / 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, 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 / FOURIER SYNTHESIS / Resolution: 1.27 Å
AuthorsKlema, V.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 15, 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_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
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
D: Peroxisomal primary amine oxidase
E: Peroxisomal primary amine oxidase
F: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)470,29957
Polymers465,7966
Non-polymers4,50451
Water112,1436225
1
A: Peroxisomal primary amine oxidase
B: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,04122
Polymers155,2652
Non-polymers1,77620
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14880 Å2
ΔGint-66 kcal/mol
Surface area44550 Å2
MethodPISA
2
C: Peroxisomal primary amine oxidase
D: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,67518
Polymers155,2652
Non-polymers1,41016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14290 Å2
ΔGint-69 kcal/mol
Surface area45080 Å2
MethodPISA
3
E: Peroxisomal primary amine oxidase
F: Peroxisomal primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,58317
Polymers155,2652
Non-polymers1,31815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14300 Å2
ΔGint-67 kcal/mol
Surface area44810 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49370 Å2
ΔGint-241 kcal/mol
Surface area128550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.887, 223.364, 103.969
Angle α, β, γ (deg.)90.00, 95.61, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 77632.617 Da / Num. of mol.: 6
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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6225 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 298 K / pH: 6
Details: 8.5% PEG 8000, 0.27 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: 0.97945
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2007
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.27→50 Å / Num. obs: 1169541 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.073 / Net I/σ(I): 23.5
Reflection shellResolution: 1.27→1.32 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.357 / % possible all: 85.3

-
Processing

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

2oov


Resolution: 1.27→31.7 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.907 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.138 58671 5 %RANDOM
Rwork0.108 ---
obs0.109 1110572 94.9 %-
all-1170625 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.06 Å2
2--0.04 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.27→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31402 0 274 6225 37901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02233837
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.891.9646255
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.85354345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19323.7741587
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.813155473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0415215
X-RAY DIFFRACTIONr_chiral_restr0.240.24901
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02126457
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7441.520567
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.761233618
X-RAY DIFFRACTIONr_scbond_it5.477313270
X-RAY DIFFRACTIONr_scangle_it7.4144.512468
X-RAY DIFFRACTIONr_rigid_bond_restr3.105333837
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.27→1.3 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 3854 -
Rwork0.174 72499 -
obs--84.16 %
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)
10.0001-0.00010.00010.0007-0.00010.0001-0-00.0001-0.0001-0-0.00010.0001-0.00010.00010.002900.00290.0001-0.00010.0032-6.837716.854.941
20.0001-0-00.0007-0.00020.0003-0-0.0001-0-0.00010.0001-00.0001-0-00.0029-0.00010.00290.000100.0031-8.294-17.624753.0671
30.00050.0002-00.0002-0.00020.00030.0001-0.0001-00-0.00010-00.0001-00.003-00.00290.000100.003237.0714-40.225433.8389
40.00030.0001-0.00020.0002-0.00030.00040000.0001-00-0-0-00.002900.00280-00.003248.6543-26.60514.3334
50.0008-0.0004-0.00030.00040.00030.0003-000.000100.0001-000.0001-00.0029-00.00280.000100.003246.774627.12433.0176
60.0003-0.0002-0.00020.00030.00020.0003-00.00010-0-0.00010.0001-0-0.00010.00010.002900.00290.0001-00.003215.898140.677712.0202
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 691
2X-RAY DIFFRACTION2B16 - 691
3X-RAY DIFFRACTION3C16 - 691
4X-RAY DIFFRACTION4D16 - 672
5X-RAY DIFFRACTION5E16 - 671
6X-RAY DIFFRACTION6F16 - 691

+
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