[English] 日本語
Yorodumi
- PDB-2mta: CRYSTAL STRUCTURE OF A TERNARY ELECTRON TRANSFER COMPLEX BETWEEN ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mta
TitleCRYSTAL STRUCTURE OF A TERNARY ELECTRON TRANSFER COMPLEX BETWEEN METHYLAMINE DEHYDROGENASE, AMICYANIN AND A C-TYPE CYTOCHROME
Components
  • (METHYLAMINE DEHYDROGENASE ...) x 2
  • AMICYANIN
  • CYTOCHROME C551I
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


methanol metabolic process / methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / aliphatic amine dehydrogenase activity / amine metabolic process / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity / iron ion binding ...methanol metabolic process / methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / aliphatic amine dehydrogenase activity / amine metabolic process / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity / iron ion binding / copper ion binding / heme binding
Similarity search - Function
Cytochrome cL / Amicyanin, Paracoccus/Methylobacterium / Amicyanin / Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain / Amine dehydrogenase heavy chain / Methylamine/Aralkylamine dehydrogenase light chain, C-terminal domain / Amine dehydrogenase light chain / Methylamine/Aralkylamine dehydrogenase light chain superfamily / Methylamine dehydrogenase, L chain ...Cytochrome cL / Amicyanin, Paracoccus/Methylobacterium / Amicyanin / Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain / Amine dehydrogenase heavy chain / Methylamine/Aralkylamine dehydrogenase light chain, C-terminal domain / Amine dehydrogenase light chain / Methylamine/Aralkylamine dehydrogenase light chain superfamily / Methylamine dehydrogenase, L chain / Methylamine dehydrogenase heavy chain (MADH) / Electron Transport Ethylamine Dehydrogenase / Methylamine/Aralkylamine dehydrogenase light chain / Amicyanin/Pseudoazurin / Quinoprotein amine dehydrogenase, beta chain-like / Blue (type 1) copper protein, plastocyanin-type / Cytochrome C oxidase, cbb3-type, subunit III / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Cupredoxins - blue copper proteins / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cupredoxin / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / HEME C / PHOSPHATE ION / Amicyanin / Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain / Cytochrome c-L
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsChen, L. / Mathews, F.S.
Citation
Journal: Science / Year: 1994
Title: Structure of an electron transfer complex: methylamine dehydrogenase, amicyanin, and cytochrome c551i.
Authors: Chen, L. / Durley, R.C. / Mathews, F.S. / Davidson, V.L.
#1: Journal: Protein Sci. / Year: 1993
Title: Crystal Structure Analysis of Amicyanin and Apoamicyanin from Paraccus Denitrificans at 2.0 Angstroms and 1.8 Angstroms Resolution
Authors: Durley, R. / Chen, L. / Lim, L.W. / Mathews, F.S. / Davidson, V.L.
#2: Journal: Protein Sci. / Year: 1993
Title: Preliminary Crystal Structure Studies of a Ternary Electron Transfer Complex between a Quinoprotein, a Blue Copper Protein, and a C-Type Cytochrome
Authors: Chen, L. / Mathews, F.S. / Davidson, V.L. / Tegoni, M. / Rivetti, C. / Rossi, G.L.
#3: 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.D. / Hol, W.G.J.
#4: 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.
History
DepositionOct 26, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 10, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_symm_contact / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_validate_symm_contact.auth_atom_id_2 / _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.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)
L: METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)
A: AMICYANIN
C: CYTOCHROME C551I
H: PHOSPHATE ION
A: COPPER (II) ION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3497
Polymers82,5724
Non-polymers7773
Water2,288127
1
H: METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)
L: METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)
A: AMICYANIN
C: CYTOCHROME C551I
hetero molecules

H: METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)
L: METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)
A: AMICYANIN
C: CYTOCHROME C551I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,69814
Polymers165,1448
Non-polymers1,5546
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)148.810, 68.850, 187.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: CIS PROLINE - PRO H 145
2: GLN C 146 - PRO C 147 OMEGA =145.73 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Components on special symmetry positions
IDModelComponents
11H--

PO4

-
Components

-
METHYLAMINE DEHYDROGENASE ... , 2 types, 2 molecules HL

#1: Protein METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)


Mass: 41063.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / References: UniProt: P29894, EC: 1.4.99.3
#2: Protein METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)


Mass: 13728.206 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / References: UniProt: P22619, EC: 1.4.99.3

-
Protein , 2 types, 2 molecules AC

#3: Protein AMICYANIN


Mass: 11505.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / References: UniProt: P22364
#4: Protein CYTOCHROME C551I


Mass: 16274.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / References: UniProt: P29899

-
Non-polymers , 4 types, 130 molecules HA

#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#7: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsTHIS IS THE FIRST TERNARY COMPLEX COMPOSED OF THREE SEQUENTIAL PROTEINS IN AN ELECTRON TRANSFER ...THIS IS THE FIRST TERNARY COMPLEX COMPOSED OF THREE SEQUENTIAL PROTEINS IN AN ELECTRON TRANSFER CHAIN. SEVERAL HYPOTHETICAL ELECTRON TRANSFER PATHWAYS BETWEEN BOTH MADH-AMICYANIN AND AMICYANIN-CYTOCHROME WERE DISCUSSED IN THE PAPER CITED ON JRNL RECORDS ABOVE.
Nonpolymer detailsTHE REDOX COFACTOR TTQ OF MADH IS LOCATED ON EACH L SUBUNIT, WHICH IS COMPRISED OF THE SIDE CHAINS ...THE REDOX COFACTOR TTQ OF MADH IS LOCATED ON EACH L SUBUNIT, WHICH IS COMPRISED OF THE SIDE CHAINS OF TWO TRYPTOPHANS ON THE L SUBUNIT, LINKED BY A COVALENT BOND BETWEEN TWO INDOLE RINGS. ONE INDOLE RING HAS AN ORTHO-QUINONE STRUCTURE. THE STRUCTURE IS CALLED TRYPTOPHAN TRYPTOPHYLQUINONE (TTQ). THE TWO ADDITIONAL OXYGEN ATOMS OF THE INDOLE RING OF TRP L 57 ARE PRESENTED HETATM GROUP OWQ.
Sequence detailsSEQUENCE ADVISORY NOTICE: AT PRESENT, THE SEQUENCE DATABASES INDICATE THAT RESIDUE 299 OF THE HEAVY ...SEQUENCE ADVISORY NOTICE: AT PRESENT, THE SEQUENCE DATABASES INDICATE THAT RESIDUE 299 OF THE HEAVY CHAIN IS LEU AND RESIDUE 300 IS LEU. THE AUTHORS FOUND THAT THEY MISREAD THE GELS AND THAT RESIDUES 299 AND 300 SHOULD BE PHE AND VAL, RESPECTIVELY. IN THIS ENTRY RESIDUE 299 IS CORRECTLY PRESENTED AS PHE BUT RESIDUE 300 IS INCORRECTLY PRESENTED AS LEU.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.61 %

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.179 / Rfactor obs: 0.179 / Highest resolution: 2.4 Å
Details: THE CURRENT MODEL CONTAINS AN AMICYANIN PORTION TRANSFORMED FROM THE MADH-AMICYANIN BINARY COMPLEX (CHEN ET AL., BIOCHEMISTRY, 1992), WHICH WAS NOT INCLUDED IN THE PHASE REFINEMENT. ONLY THE ...Details: THE CURRENT MODEL CONTAINS AN AMICYANIN PORTION TRANSFORMED FROM THE MADH-AMICYANIN BINARY COMPLEX (CHEN ET AL., BIOCHEMISTRY, 1992), WHICH WAS NOT INCLUDED IN THE PHASE REFINEMENT. ONLY THE CA OF EACH RESIDUE AND THE COPPER ATOM ARE INCLUDED AT THIS STAGE. THE CYTOCHROME PORTION OF THE CURRENT MODEL IS SIMULATED FROM CYTOCHROME C551 DEPOSITED IN PROTEIN DATA BANK (MUTSUURA ET AL., J. MOL. BIOL. 1982). ONLY THE HEME GROUP WAS BUILT TO FIT THE ELECTRON DENSITY AND IS SUBMITTED.
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5807 0 47 127 5981
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.58
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

+
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://pdbjlvh1.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