5FCD | pdb_00005fcd

Crystal structure of MccD protein

PDB DOI: https://doi.org/10.2210/pdb5FCD/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2015-12-15 Released: 2015-12-30
Deposition Author(s): Nocek, B., Jedrzejczak, R., Anderson, W.F., Severinov, K., Dubiley, S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.223 (Depositor), 0.226 (DCC)
R-Value Work:
0.199 (Depositor), 0.199 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of MccD protein.

Nocek, B., Jedrzejczak, R., Anderson, W.F., Severinov, K., Dubiley, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 64.4 kDa
Atom Count: 3,973
Modeled Residue Count: 467
Deposited Residue Count: 545
Unique protein chains: 3

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UNK-UNK-UNK-MSE-UNK	A [auth D]	5	Escherichia coli	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UNK-UNK-UNK-UNK-MSE-UNK	B [auth E]	6	Escherichia coli	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MccD	C [auth A], D [auth B]	267	Escherichia coli	Mutation(s): 0 Gene Names: mccD
UniProt
Find proteins for Q83Y56 (Escherichia coli) Explore Q83Y56 Go to UniProtKB: Q83Y56
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q83Y56
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A [auth D]	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET
UNK Query on UNK	A [auth D]	L-PEPTIDE LINKING	C₄ H₉ N O₂		--

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.223 (Depositor), 0.226 (DCC)
R-Value Work: 0.199 (Depositor), 0.199 (DCC)
R-Value Observed: 0.200 (Depositor)

Diffraction Data:

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.1	α = 90
b = 95.1	β = 90
c = 128.685	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-12-30

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2015-12-30
Type: Initial release
Version 1.1: 2017-02-08
Changes: Structure summary
Version 1.2: 2024-11-13
Changes: Data collection, Database references, Structure summary