6KG3 | pdb_00006kg3

Crystal structure of Nicotinic acid mononucleotide adenylyltransferase mutant P22K/Y84V/Y118D/C132Q/W176F from Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb6KG3/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli NCCP15648
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-07-10 Released: 2020-07-15
Deposition Author(s): Xue, S., Zhao, Z., Wang, X., Feng, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.08 Å
R-Value Free:
0.268 (Depositor), 0.269 (DCC)
R-Value Work:
0.241 (Depositor), 0.243 (DCC)
R-Value Observed:
0.242 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Nicotinic acid mononucleotide adenylyltransferase mutant P22K/Y84V/Y118D/C132Q/W176F from Escherichia coli

Xue, S., Feng, Y., Zhao, Z., Wang, X.

To be published.

Macromolecule Content

Total Structure Weight: 146.76 kDa
Atom Count: 10,158
Modeled Residue Count: 1,257
Deposited Residue Count: 1,278
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable nicotinate-nucleotide adenylyltransferase	A, B, C, D, E A, B, C, D, E, F	213	Escherichia coli NCCP15648	Mutation(s): 5 Gene Names: nadD, A610_610 EC: 2.7.7.18
UniProt
Find proteins for P0A752 (Escherichia coli (strain K12)) Explore P0A752 Go to UniProtKB: P0A752
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A752
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.08 Å
R-Value Free: 0.268 (Depositor), 0.269 (DCC)
R-Value Work: 0.241 (Depositor), 0.243 (DCC)
R-Value Observed: 0.242 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.912	α = 90
b = 129.176	β = 103.177
c = 105.32	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-07-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-07-15
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.