2Q0M | pdb_00002q0m

Tricarbonylmanganese(I)-lysozyme complex : a structurally characterized organometallic protein

PDB DOI: https://doi.org/10.2210/pdb2Q0M/pdb

Classification: HYDROLASE
Organism(s): Gallus gallus
Mutation(s): No

Deposited: 2007-05-22 Released: 2007-12-11
Deposition Author(s): Razavet, M., Artero, V., Cavazza, C., Oudart, Y., Fontecilla-Camps, J.C., Fontecave, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.249 (Depositor), 0.250 (DCC)
R-Value Work:
0.206 (Depositor), 0.207 (DCC)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Tricarbonylmanganese(I)-lysozyme complex: a structurally characterized organometallic protein.

Razavet, M., Artero, V., Cavazza, C., Oudart, Y., Lebrun, C., Fontecilla-Camps, J.C., Fontecave, M.

(2007) Chem Commun (Camb) : 2805-2807

PubMed: 17609782 Search on PubMed
DOI: https://doi.org/10.1039/b703887a
Primary Citation Related Structures:
2Q0M

PubMed Abstract:
The reaction of the new and structurally characterized covalent {Mn(CO)(3)(H(2)O)(2)}(+)-lysozyme adduct with NiS(4) and NiN(2)S(2) complexes generates binuclear Ni-Mn complexes; relevance to the reactivity of the protein-bound {Fe(CO)(CN)(2)} intermediate during maturation of [NiFe] hydrogenases is discussed.

Organizational Affiliation

Laboratoire de Chimie et Biologie des Métaux, Université Joseph Fourier, Grenoble, France.

Macromolecule Content

Total Structure Weight: 14.68 kDa
Atom Count: 1,109
Modeled Residue Count: 129
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A [auth X]	129	Gallus gallus	Mutation(s): 0 EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TFS Query on TFS Download:Ideal Coordinates CCD File SDF format, chain H [auth X] MOL2 format, chain H [auth X] mmCIF format, chain H [auth X]	H [auth X]	trifluoromethanesulfonic acid C H F₃ O₃ S ITMCEJHCFYSIIV-UHFFFAOYSA-N		Interactions Focus chain H [auth X] Interactions & Density Focus chain H [auth X]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain D [auth X] MOL2 format, chain D [auth X] mmCIF format, chain D [auth X]	D [auth X]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth X] Interactions & Density Focus chain D [auth X]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]
CMO Query on CMO Download:Ideal Coordinates CCD File SDF format, chain E [auth X] SDF format, chain F [auth X] SDF format, chain G [auth X] MOL2 format, chain E [auth X] MOL2 format, chain F [auth X] MOL2 format, chain G [auth X] mmCIF format, chain E [auth X] mmCIF format, chain F [auth X] mmCIF format, chain G [auth X]	E [auth X], F [auth X], G [auth X]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N		Interactions Focus chain E [auth X] Focus chain F [auth X] Focus chain G [auth X] Interactions & Density Focus chain E [auth X] Focus chain F [auth X] Focus chain G [auth X]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth X] MOL2 format, chain C [auth X] mmCIF format, chain C [auth X]	C [auth X]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth X] Interactions & Density Focus chain C [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.249 (Depositor), 0.250 (DCC)
R-Value Work: 0.206 (Depositor), 0.207 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.542	α = 90
b = 79.542	β = 90
c = 36.392	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
XDS	data reduction
XDS	data scaling
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-12-11

Deposition Author(s):

Fontecilla-Camps, J.C.

Fontecave, M.

Revision History (Full details and data files)

Version 1.0: 2007-12-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-18
Changes: Advisory, Refinement description
Version 1.3: 2023-07-26
Changes: Advisory, Database references, Derived calculations
Version 1.4: 2024-10-30
Changes: Data collection, Structure summary