8KFK | pdb_00008kfk

Crystal Structure of Imine Reductase from Paenibacillus mucilaginosus

PDB DOI: https://doi.org/10.2210/pdb8KFK/pdb

Classification: OXIDOREDUCTASE
Organism(s): Paenibacillus mucilaginosus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-08-15 Released: 2024-08-21
Deposition Author(s): Wu, K.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.240 (Depositor), 0.241 (DCC)
R-Value Work:
0.207 (Depositor), 0.208 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal Structure of Imine Reductase from Paenibacillus mucilaginosus

Wu, K.

To be published.

Macromolecule Content

Total Structure Weight: 67.53 kDa
Atom Count: 4,496
Modeled Residue Count: 571
Deposited Residue Count: 620
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconate dehydrogenase	A, B	310	Paenibacillus mucilaginosus	Mutation(s): 0 Gene Names: B2K_07400
UniProt
Find proteins for I0BDU9 (Paenibacillus mucilaginosus K02) Explore I0BDU9 Go to UniProtKB: I0BDU9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I0BDU9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P4C Query on P4C Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL C₁₄ H₂₈ O₈ CTLLATPOKUEFSQ-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.240 (Depositor), 0.241 (DCC)
R-Value Work: 0.207 (Depositor), 0.208 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.771	α = 90
b = 133.771	β = 90
c = 62.23	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2024-08-21
Type: Initial release

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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.