5I1W | pdb_00005i1w

Crystal structure of CrmK, a flavoenzyme involved in the shunt product recycling mechanism in caerulomycin biosynthesis

PDB DOI: https://doi.org/10.2210/pdb5I1W/pdb

Classification: OXIDOREDUCTASE
Organism(s): Actinoalloteichus sp. WH1-2216-6
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-02-07 Released: 2017-02-15
Deposition Author(s): Picard, M.-E., Barma, J., Shi, R.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.213 (Depositor), 0.218 (DCC)
R-Value Work:
0.168 (Depositor), 0.176 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Biochemical and structural insights into flavoenzyme CrmK reveals a shunt product recycling mechanism in caerulomycin biosynthesis

Zhu, Y., Picard, M.-E., Mei, X., Zhang, Q., Barma, J., Murphy Despres, X., Couture, M., Zhu, W., Zhang, C., Shi, R.

To be published.

Macromolecule Content

Total Structure Weight: 225.09 kDa
Atom Count: 16,449
Modeled Residue Count: 1,992
Deposited Residue Count: 2,000
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CrmK	A, B, C, D	500	Actinoalloteichus sp. WH1-2216-6	Mutation(s): 0
UniProt
Find proteins for H8Y6P5 (Actinoalloteichus sp. WH1-2216-6) Explore H8Y6P5 Go to UniProtKB: H8Y6P5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H8Y6P5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
67L Query on 67L Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C]	6-(hydroxymethyl)[2,2'-bipyridin]-4-ol C₁₁ H₁₀ N₂ O₂ HKHZGZONLACWBE-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C]
67K Query on 67K Download:Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	4-hydroxy[2,2'-bipyridine]-6-carbaldehyde C₁₁ H₈ N₂ O₂ FFOWHRKNAPHKGV-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.213 (Depositor), 0.218 (DCC)
R-Value Work: 0.168 (Depositor), 0.176 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.11	α = 94.73
b = 95.2	β = 96.56
c = 98.04	γ = 105.2

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-02-15

Deposition Author(s):

Picard, M.-E.

Barma, J.

Shi, R.

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2017-02-15
Type: Initial release
Version 1.1: 2017-09-13
Changes: Author supporting evidence
Version 1.2: 2020-01-08
Changes: Author supporting evidence, Derived calculations
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-23
Changes: Structure summary