2J57

X-ray reduced Paraccocus denitrificans methylamine dehydrogenase N- quinol in complex with amicyanin.

PDB DOI: https://doi.org/10.2210/pdb2J57/pdb

Classification: OXIDOREDUCTASE
Organism(s): Paracoccus denitrificans
Mutation(s): No

Deposited: 2006-09-12 Released: 2007-01-23
Deposition Author(s): Pearson, A.R., Pahl, R., Davidson, V.L., Wilmot, C.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.241
R-Value Work: 0.179
R-Value Observed: 0.183

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Tracking X-Ray-Derived Redox Changes in Crystals of a Methylamine Dehydrogenase/Amicyanin Complex Using Single-Crystal Uv/Vis Microspectrophotometry.

Pearson, A.R., Pahl, R., Kovaleva, E.G., Davidson, V.L., Wilmot, C.M.

(2007) J Synchrotron Radiat 14: 92

PubMed: 17211075 Search on PubMed
DOI: https://doi.org/10.1107/S0909049506051259
Primary Citation of Related Structures:
2J55, 2J56, 2J57

PubMed Abstract:
X-ray exposure during crystallographic data collection can result in unintended redox changes in proteins containing functionally important redox centers. In order to directly monitor X-ray-derived redox changes in trapped oxidative half-reaction intermediates of Paracoccus denitrificans methylamine dehydrogenase, a commercially available single-crystal UV/Vis microspectrophotometer was installed on-line at the BioCARS beamline 14-BM-C at the Advanced Photon Source, Argonne, USA. Monitoring the redox state of the intermediates during X-ray exposure permitted the creation of a general multi-crystal data collection strategy to generate true structures of each redox intermediate.

Organizational Affiliation

Department of Biochemistry, Molecular Biology and Biophysics, The University of Minnesota, Minneapolis, MN 55455, USA.

Macromolecule Content

Total Structure Weight: 272.91 kDa
Atom Count: 20,786
Modelled Residue Count: 2,448
Deposited Residue Count: 2,488
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AMICYANIN	A, B, C, D	105	Paracoccus denitrificans	Mutation(s): 0
UniProt
Find proteins for P22364 (Paracoccus denitrificans) Explore P22364 Go to UniProtKB: P22364
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22364
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
METHYLAMINE DEHYDROGENASE HEAVY CHAIN	E [auth G], F [auth H], G [auth I], H [auth J]	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29894
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
METHYLAMINE DEHYDROGENASE LIGHT CHAIN	I [auth K], J [auth L], K [auth M], L [auth N]	131	Paracoccus denitrificans	Mutation(s): 0 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22619
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain P [auth D] SDF format, chain M [auth A] SDF format, chain O [auth C] MOL2 format, chain N [auth B] MOL2 format, chain P [auth D] MOL2 format, chain M [auth A] MOL2 format, chain O [auth C] mmCIF format, chain N [auth B] mmCIF format, chain P [auth D] mmCIF format, chain M [auth A] mmCIF format, chain O [auth C]	M [auth A], N [auth B], O [auth C], P [auth D]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TQQ Query on TQQ	I [auth K], J [auth L], K [auth M], L [auth N]	L-PEPTIDE LINKING	C₁₁ H₁₁ N₃ O₃		TRP

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.241
R-Value Work: 0.179
R-Value Observed: 0.183
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.131	α = 90
b = 123.439	β = 90
c = 246.92	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-01-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-01-23
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Other, Structure summary