[English] 日本語
Yorodumi
- PDB-1mda: CRYSTAL STRUCTURE OF AN ELECTRON-TRANSFER COMPLEX BETWEEN METHYLA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mda
TitleCRYSTAL STRUCTURE OF AN ELECTRON-TRANSFER COMPLEX BETWEEN METHYLAMINE DEHYDROGENASE AND AMICYANIN
Components
  • AMICYANIN
  • METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)
  • METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Amicyanin, Paracoccus/Methylobacterium / Amicyanin / : / Electron Transport Ethylamine Dehydrogenase / Methylamine/Aralkylamine dehydrogenase light chain / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site ...Amicyanin, Paracoccus/Methylobacterium / Amicyanin / : / Electron Transport Ethylamine Dehydrogenase / Methylamine/Aralkylamine dehydrogenase light chain / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / YVTN repeat-like/Quinoprotein amine dehydrogenase / Cupredoxin / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / : / Amicyanin
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsChen, L. / Durley, R. / Mathews, F.S.
Citation
Journal: Biochemistry / Year: 1992
Title: Crystal structure of an electron-transfer complex between methylamine dehydrogenase and amicyanin.
Authors: Chen, L. / Durley, R. / Poliks, B.J. / Hamada, K. / Chen, Z. / Mathews, F.S. / Davidson, V.L. / Satow, Y. / Huizinga, E. / Vellieux, F.M. / Hol, W.G.J.
#1: Journal: Proteins / Year: 1992
Title: Three-Dimensional Structure of the Quinoprotein Methylamine Dehydrogenase from Paracoccus Denitrificans Determined by Molecular Replacement at 2.8 Angstroms Resolution
Authors: Chen, L. / Mathews, F.S. / Davidson, V.L. / Huizinga, E.G. / Vellieux, F.M.D. / Hol, W.G.J.
#2: Journal: Science / Year: 1991
Title: A New Cofactor in a Prokaryotic Enzyme: Tryptophan Tryptophylquinone as the Redox Prosthetic Group in Methylamine Dehydrogenase
Authors: Mcintire, W.S. / Wemmer, D.E. / Chistoserdov, A. / Lidstrom, M.E.
#3: Journal: Embo J. / Year: 1989
Title: Structure of Quinoprotein Methylamine Dehydrogenase at 2.25 Angstroms Resolution
Authors: Vellieux, F.M.D. / Huitema, F. / Groendijk, H. / Kalk, K.H. / Frank Jzn., J. / Jongejan, J.A. / Duine, J.A. / Petratos, K. / Drenth, J. / Hol, W.G.J.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1990
Title: Structure Determination of Quinoprotein Methylamine Dehydrogenase from Thiobacillus Versutus
Authors: Vellieux, F.M.D. / Kalk, K.H. / Drenth, J. / Hol, W.G.
History
DepositionMar 2, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_ref_seq_dif.details / _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
H: METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)
L: METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)
J: METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)
M: METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)
A: AMICYANIN
B: AMICYANIN
A: COPPER (II) ION
B: COPPER (II) ION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,5438
Polymers122,4166
Non-polymers1272
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.700, 124.700, 247.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: CIS PROLINE - PRO A 6 / 2: CIS PROLINE - PRO B 6
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.3439, -0.7653, -0.5441), (-0.7652, -0.5643, 0.3099), (-0.5442, 0.3098, -0.7797)
Vector: 111.104, 92.613, 144.168)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *H* AND *L* WHEN APPLIED TO CHAIN *J* AND *M*, RESPECTIVELY.

-
Components

#1: Protein METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)


Mass: 36866.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / References: EC: 1.4.99.3
#2: Protein METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)


Mass: 13080.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / References: PIR: A44544, EC: 1.4.99.3
#3: Protein AMICYANIN


Mass: 11260.903 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / References: UniProt: P22364
#4: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
Compound detailsTHE REDOX CENTERS OF MADH ARE LOCATED ON EACH L SUBUNIT. EACH IS COMPOSED OF THE SIDE CHAINS OF TWO ...THE REDOX CENTERS OF MADH ARE LOCATED ON EACH L SUBUNIT. EACH IS COMPOSED OF THE SIDE CHAINS OF TWO AMINO ACIDS ON THE L SUBUNIT, BOTH ARE TRYPTOPHANS, LINKED BY COVALENT BOND BETWEEN TWO INDOLE RINGS. ONE INDOLE RING HAS AN ORTHO-QUINONE STRUCTURE. THE STRUCTURE OF THIS DOUBLE-TRYPTOPHAN SYSTEM IS CALLED TRYPTOPHAN TRYPTOPHYL-QUINONE (TRP + OWQ).
Sequence detailsTHIS IS AN X-RAY DETERMINED SEQUENCE WHICH WAS ESTABLISHED ON THE BASIS OF THE ELECTRON DENSITY DUE ...THIS IS AN X-RAY DETERMINED SEQUENCE WHICH WAS ESTABLISHED ON THE BASIS OF THE ELECTRON DENSITY DUE TO THE LACK OF AN AMINO ACID SEQUENCE. SEE REFERENCE 4 ABOVE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.67 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
22.4 Msodium phosphate1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Rmerge(I) obs: 0.084

-
Processing

Software
NameClassification
PROLSQrefinement
TNTrefinement
RefinementRfactor obs: 0.285 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8565 0 2 0 8567
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d3.2
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.5 Å / Rfactor obs: 0.285
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 45 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg3.2

+
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