[English] 日本語
Yorodumi
- PDB-5zpq: Copper amine oxidase from Arthrobacter globiformis anaerobically ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zpq
TitleCopper amine oxidase from Arthrobacter globiformis anaerobically reduced by phenylethylamine at pH 9 at 288 K (1)
ComponentsPhenylethylamine oxidase
KeywordsOXIDOREDUCTASE / COPPER AMINE OXIDASE / TOPAQUINONE / TPQ
Function / homology
Function and homology information


primary-amine oxidase / primary methylamine oxidase activity / amine metabolic process / quinone binding / copper ion binding
Similarity search - Function
: / AGAO-like 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 ...: / AGAO-like 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
COPPER (II) ION / PHENYLACETALDEHYDE / Phenylethylamine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 Å
AuthorsMurakawa, T. / Baba, S. / Kawano, Y. / Hayashi, H. / Yano, T. / Tanizawa, K. / Kumasaka, T. / Yamamoto, M. / Okajima, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)0294 Japan
JSPS KAKENHI17K07317, JP26440037, JP23770127, JP15K05573, JP16KT0055 Japan
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: In crystallothermodynamic analysis of conformational change of the topaquinone cofactor in bacterial copper amine oxidase.
Authors: Murakawa, T. / Baba, S. / Kawano, Y. / Hayashi, H. / Yano, T. / Kumasaka, T. / Yamamoto, M. / Tanizawa, K. / Okajima, T.
History
DepositionApr 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 22, 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_conn_type
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_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.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_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.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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phenylethylamine oxidase
B: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,38811
Polymers137,8282
Non-polymers5609
Water18,1771009
1
A: Phenylethylamine oxidase
hetero molecules

A: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,41112
Polymers137,8282
Non-polymers58310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14470 Å2
ΔGint-69 kcal/mol
Surface area40580 Å2
MethodPISA
2
B: Phenylethylamine oxidase
hetero molecules

B: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,36510
Polymers137,8282
Non-polymers5388
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area14590 Å2
ΔGint-80 kcal/mol
Surface area40720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.605, 64.262, 158.870
Angle α, β, γ (deg.)90.000, 117.030, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1139-

HOH

21A-1223-

HOH

31A-1295-

HOH

41B-1201-

HOH

51B-1216-

HOH

61B-1280-

HOH

71B-1303-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Phenylethylamine oxidase / Primary amine oxidase


Mass: 68913.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Plasmid: pepo-2 / Production host: Escherichia coli (E. coli) / Strain (production host): CD03 / References: UniProt: P46881, primary-amine oxidase

-
Non-polymers , 5 types, 1018 molecules

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


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-HY1 / PHENYLACETALDEHYDE


Mass: 120.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1009 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.29 %
Crystal growTemperature: 289 K / Method: microdialysis / pH: 7.4 / Details: 1.05M potassium-sodium tartrate, 25mM HEPES

-
Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 148084 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 19.88 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.06 / Rrim(I) all: 0.113 / Χ2: 1.83 / Net I/σ(I): 7.3 / Num. measured all: 521039
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.883.20.63973670.7180.4180.7661.16999.7
1.88-1.923.30.53773530.80.350.6441.24799.9
1.92-1.953.30.46573750.8320.3020.5561.27399.9
1.95-1.993.30.39473650.8740.2540.471.38999.9
1.99-2.043.40.34773420.90.2220.4131.45799.9
2.04-2.083.40.31273530.9130.1980.371.4899.9
2.08-2.143.50.28173870.9270.1770.3331.553100
2.14-2.193.50.24873430.9430.1550.2941.62199.9
2.19-2.263.60.22373810.950.1380.2631.674100
2.26-2.333.60.273780.9580.1230.2351.713100
2.33-2.413.70.18274070.9660.1110.2141.75100
2.41-2.513.70.17173600.9680.1040.2011.78999.9
2.51-2.633.70.15474330.9730.0930.181.899100
2.63-2.763.70.13674020.9760.0830.162.06499.9
2.76-2.943.70.12174160.9810.0740.1422.447100
2.94-3.163.60.10374110.9860.0630.1212.77799.9
3.16-3.483.60.08474170.990.0530.13.118100
3.48-3.993.60.06574830.9940.040.0762.71499.9
3.99-5.023.60.03974730.9970.0240.0461.57899.5
5.02-503.50.03376380.9980.0210.041.48599.5

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IU7

1iu7


Resolution: 1.849→39.673 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 17.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.173 7368 4.98 %
Rwork0.1454 140586 -
obs0.1467 147954 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.04 Å2 / Biso mean: 24.753 Å2 / Biso min: 6.82 Å2
Refinement stepCycle: final / Resolution: 1.849→39.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9738 0 31 1009 10778
Biso mean--25.37 38.27 -
Num. residues----1240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610145
X-RAY DIFFRACTIONf_angle_d0.87313839
X-RAY DIFFRACTIONf_chiral_restr0.061490
X-RAY DIFFRACTIONf_plane_restr0.0051849
X-RAY DIFFRACTIONf_dihedral_angle_d16.1756017
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8487-1.86970.28792350.26124611484699
1.8697-1.89170.28342700.245146894959100
1.8917-1.91470.24952390.228446344873100
1.9147-1.9390.24222410.219346504891100
1.939-1.96450.22292360.194946984934100
1.9645-1.99140.19582800.180646374917100
1.9914-2.01990.18792430.172846494892100
2.0199-2.050.19052440.173746064850100
2.05-2.0820.20232560.166447054961100
2.082-2.11620.19532900.166246414931100
2.1162-2.15270.2022650.164646134878100
2.1527-2.19180.18662420.15746804922100
2.1918-2.23390.20322370.155646854922100
2.2339-2.27950.18522410.152746644905100
2.2795-2.32910.19092340.149847064940100
2.3291-2.38330.17642220.150547274949100
2.3833-2.44290.17122460.150246494895100
2.4429-2.50890.19092420.151446744916100
2.5089-2.58270.18732530.145747064959100
2.5827-2.66610.18842370.146147114948100
2.6661-2.76130.17942440.143546934937100
2.7613-2.87190.19232250.148346854910100
2.8719-3.00250.19012360.151447444980100
3.0025-3.16080.15292410.14546904931100
3.1608-3.35870.15352440.134147214965100
3.3587-3.61790.14212550.119747094964100
3.6179-3.98160.12642720.104147074979100
3.9816-4.55710.13392320.100847444976100
4.5571-5.73870.12392320.111347564988100
5.7387-39.68250.17282340.15374802503697
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)
10.48810.334-0.03770.4538-0.1150.03920.0669-0.10020.03440.2271-0.1040.1555-0.0967-0.1391-0.09880.23380.05380.03680.23-0.06730.1623-17.980922.750934.7103
20.3135-0.1049-0.13910.15170.10050.364-0.0179-0.3146-0.01880.1477-0.01070.0422-0.04020.1162-0.0070.1747-0.0293-0.01270.2510.01430.1676.674113.057537.3794
30.27330.0432-0.02930.263-0.01880.87940.007-0.02290.01620.0208-0.0114-0.0008-0.1-0.06880.00030.09880.0076-0.00180.0791-0.00330.1132-5.99316.445210.1169
40.1298-0.0538-0.02610.1459-0.01940.01250.03480.065-0.0131-0.1552-0.0281-0.0992-0.03530.1584-0.00760.1676-0.01820.03570.1950.0330.1516-16.5124-9.154636.8466
50.3032-0.0316-0.0830.2237-0.02470.7190.01630.0588-0.0123-0.0313-0.0167-0.0058-0.04210.02560.00120.08920.0067-0.00250.0667-0.00470.1074-32.0622-16.074355.1414
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 72 )A9 - 72
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 191 )A73 - 191
3X-RAY DIFFRACTION3chain 'A' and (resid 192 through 628 )A192 - 628
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 72 )B9 - 72
5X-RAY DIFFRACTION5chain 'B' and (resid 73 through 628 )B73 - 628

+
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