2GC4 | pdb_00002gc4

Structural comparison of the oxidized ternary electron transfer complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans with the substrate-reduced, copper free complex at 1.9 A resolution.

PDB DOI: https://doi.org/10.2210/pdb2GC4/pdb

Classification: Oxidoreductase, Electron transport
Organism(s): Paracoccus denitrificans
Mutation(s): Yes

Deposited: 2006-03-13 Released: 2006-11-28
Deposition Author(s): Chen, Z., Durley, R., Davidson, V.L., Mathews, F.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.197 (Depositor), 0.192 (DCC)
R-Value Work:
0.173 (Depositor), 0.169 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structural comparison of the oxidized ternary electron transfer complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans with the substrate-reduced, copper free complex at 1.9 A resolution.

Chen, Z., Durley, R., Davidson, V.L., Mathews, F.S.

To be published.

Macromolecule Content

Total Structure Weight: 340.58 kDa
Atom Count: 24,820
Modeled Residue Count: 3,036
Deposited Residue Count: 3,076
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylamine dehydrogenase heavy chain	A, E, I, M	386	Paracoccus denitrificans	Mutation(s): 0 EC: 1.4.99.3 (PDB Primary Data), 1.4.9.1 (UniProt)
UniProt
Find proteins for P29894 (Paracoccus denitrificans) Explore P29894 Go to UniProtKB: P29894
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29894
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylamine dehydrogenase light chain	B, F, J, N	131	Paracoccus denitrificans	Mutation(s): 1 EC: 1.4.99.3 (PDB Primary Data), 1.4.9.1 (UniProt)
UniProt
Find proteins for P22619 (Paracoccus denitrificans) Explore P22619 Go to UniProtKB: P22619
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22619
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Amicyanin	C, G, K, O	105	Paracoccus denitrificans	Mutation(s): 0
UniProt
Find proteins for P22364 (Paracoccus denitrificans) Explore P22364 Go to UniProtKB: P22364
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22364
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c-L	D, H, L, P	147	Paracoccus denitrificans	Mutation(s): 0
UniProt
Find proteins for P29899 (Paracoccus denitrificans) Explore P29899 Go to UniProtKB: P29899
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29899
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain Y [auth L] SDF format, chain V [auth H] SDF format, chain S [auth D] SDF format, chain BA [auth P] MOL2 format, chain Y [auth L] MOL2 format, chain V [auth H] MOL2 format, chain S [auth D] MOL2 format, chain BA [auth P] mmCIF format, chain Y [auth L] mmCIF format, chain V [auth H] mmCIF format, chain S [auth D] mmCIF format, chain BA [auth P]	BA [auth P], S [auth D], V [auth H], Y [auth L]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain BA [auth P] Focus chain S [auth D] Focus chain V [auth H] Focus chain Y [auth L] Interactions & Density Focus chain BA [auth P] Focus chain S [auth D] Focus chain V [auth H] Focus chain Y [auth L]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain Z [auth O] SDF format, chain W [auth K] SDF format, chain T [auth G] SDF format, chain Q [auth C] MOL2 format, chain Z [auth O] MOL2 format, chain W [auth K] MOL2 format, chain T [auth G] MOL2 format, chain Q [auth C] mmCIF format, chain Z [auth O] mmCIF format, chain W [auth K] mmCIF format, chain T [auth G] mmCIF format, chain Q [auth C]	Q [auth C], T [auth G], W [auth K], Z [auth O]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain Q [auth C] Focus chain T [auth G] Focus chain W [auth K] Focus chain Z [auth O] Interactions & Density Focus chain Q [auth C] Focus chain T [auth G] Focus chain W [auth K] Focus chain Z [auth O]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain X [auth L] SDF format, chain U [auth H] SDF format, chain R [auth D] SDF format, chain AA [auth P] MOL2 format, chain X [auth L] MOL2 format, chain U [auth H] MOL2 format, chain R [auth D] MOL2 format, chain AA [auth P] mmCIF format, chain X [auth L] mmCIF format, chain U [auth H] mmCIF format, chain R [auth D] mmCIF format, chain AA [auth P]	AA [auth P], R [auth D], U [auth H], X [auth L]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth P] Focus chain R [auth D] Focus chain U [auth H] Focus chain X [auth L] Interactions & Density Focus chain AA [auth P] Focus chain R [auth D] Focus chain U [auth H] Focus chain X [auth L]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TRQ Query on TRQ	B, F, J, N	L-PEPTIDE LINKING	C₁₁ H₁₀ N₂ O₄		TRP

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.197 (Depositor), 0.192 (DCC)
R-Value Work: 0.173 (Depositor), 0.169 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.368	α = 90
b = 188.979	β = 99.74
c = 128.836	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-11-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-11-28
Type: Initial release
Version 1.1: 2008-05-05
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2021-03-03
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-08-30
Changes: Data collection, Database references, Refinement description