5FD8

Crystal Structure of MccF-like Protein (BA_5613) in complex with ASA (alanyl sulfamoyl adenylates)

PDB DOI: https://doi.org/10.2210/pdb5FD8/pdb

Classification: HYDROLASE
Organism(s): Bacillus anthracis str. Ames
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., Severinov, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 ?
R-Value Free: 0.200
R-Value Work: 0.169
R-Value Observed: 0.171

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of MccF-like Protein (BA_5613) in complex with ASA ( (alanyl sulfamoyl adenylates)

Nocek, B., Severinov, K., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 75.5 kDa
Atom Count: 5,493
Modelled Residue Count: 660
Deposited Residue Count: 662
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LD-carboxypeptidase family protein	A, B	331	Bacillus anthracis str. Ames	Mutation(s): 0 Gene Names: yocD
UniProt
Find proteins for A0A6L8PVW7 (Bacillus anthracis) Explore A0A6L8PVW7 Go to UniProtKB: A0A6L8PVW7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6L8PVW7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A5A Query on A5A Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	'5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE C₁₃ H₁₉ N₇ O₇ S CWWYMWDIYBJVLP-YTMOPEAISA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 ?
R-Value Free: 0.200
R-Value Work: 0.169
R-Value Observed: 0.171
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/m35fd8

Unit Cell:

Length ( ? )	Angle ( ? )
a = 58.777	α = 90
b = 83.683	β = 90
c = 130.845	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SBC-Collect	data collection
HKL-3000	data scaling
SHELX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-12-30

Deposition Author(s):

Nocek, B.

Severinov, K.

Joachimiak, A.

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: 2016-01-13
Changes: Other
Version 1.2: 2017-11-22
Changes: Derived calculations, Refinement description
Version 1.3: 2024-10-23
Changes: Data collection, Database references, Structure summary

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5FD8

Crystal Structure of MccF-like Protein (BA_5613) in complex with ASA (alanyl sulfamoyl adenylates)

Crystal Structure of MccF-like Protein (BA_5613) in complex with ASA ( (alanyl sulfamoyl adenylates)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)