6LAC | pdb_00006lac

The structural basis of the beta-carbonic anhydrase CafD (C39A mutant) of the filamentous fungus Aspergillus fumigatus

PDB DOI: https://doi.org/10.2210/pdb6LAC/pdb

Classification: LYASE
Organism(s): Aspergillus fumigatus Af293
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-11-12 Released: 2019-11-27
Deposition Author(s): Jiin, M.S., Kim, S., Kim, N.J., Hong, S., Kim, S., Sung, J.
Funding Organization(s): National Research Foundation (Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.210 (Depositor), 0.210 (DCC)
R-Value Work:
0.191 (Depositor), 0.200 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The structural analysis of non-catalytic zinc binding site in the minor beta-carbonic anhydrase CafD

Jin, M.S., Kim, S., Kim, N.J., Hong, S., Kim, S., Sung, J.

To be published.

Macromolecule Content

Total Structure Weight: 40.53 kDa
Atom Count: 2,831
Modeled Residue Count: 342
Deposited Residue Count: 362
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase	A, B	181	Aspergillus fumigatus Af293	Mutation(s): 1 Gene Names: AFUA_8G06554 EC: 4.2.1.1
UniProt
Find proteins for A4DA31 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)) Explore A4DA31 Go to UniProtKB: A4DA31
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4DA31
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.210 (Depositor), 0.210 (DCC)
R-Value Work: 0.191 (Depositor), 0.200 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.085	α = 90
b = 57.505	β = 111.23
c = 72.733	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-11-27

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	NRF-2017R1A2B4003278
National Research Foundation (Korea)	Korea, Republic Of	NRF-2017M3A9F6029753

Revision History (Full details and data files)

Version 1.0: 2019-11-27
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.