5JR3 | pdb_00005jr3

Crystal structure of carminomycin-4-O-methyltransferase DnrK in complex with SAH and 4-methylumbelliferone

PDB DOI: https://doi.org/10.2210/pdb5JR3/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces peucetius
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-05-05 Released: 2016-06-01
Deposition Author(s): Wang, F., Johnson, B.R., Huber, T.D., Singh, S., Thorson, J.S., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.180 (Depositor), 0.184 (DCC)
R-Value Work:
0.160 (Depositor), 0.162 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of carminomycin-4-O-methyltransferase DnrK in complex with SAH and 4-methylumbelliferone (to be published)

Wang, F., Johnson, B.R., Huber, T.D., Singh, S., Thorson, J.S., Phillips Jr., G.N.

To be published.

Macromolecule Content

Total Structure Weight: 125.84 kDa
Atom Count: 9,044
Modeled Residue Count: 1,027
Deposited Residue Count: 1,128
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carminomycin 4-O-methyltransferase DnrK	A, B, C	376	Streptomyces peucetius	Mutation(s): 0 Gene Names: dnrK EC: 2.1.1.292
UniProt
Find proteins for Q06528 (Streptomyces peucetius) Explore Q06528 Go to UniProtKB: Q06528
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q06528
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain R [auth C] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain R [auth C] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain R [auth C]	D [auth A], J [auth B], R [auth C]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain R [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain R [auth C]
4MU Query on 4MU Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain S [auth C] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain S [auth C] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain S [auth C]	E [auth A], K [auth B], S [auth C]	7-hydroxy-4-methyl-2H-chromen-2-one C₁₀ H₈ O₃ HSHNITRMYYLLCV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain S [auth C] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain S [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C]	F [auth A] G [auth A] H [auth A] I [auth A] L [auth B] F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], T [auth C], U [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.180 (Depositor), 0.184 (DCC)
R-Value Work: 0.160 (Depositor), 0.162 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.16	α = 90
b = 111.098	β = 120.02
c = 116.225	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-06-01

Deposition Author(s):

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U01GM098248

Revision History (Full details and data files)

Version 1.0: 2016-06-01
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2019-12-25
Changes: Author supporting evidence
Version 2.0: 2023-03-22
Changes: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
Version 2.1: 2023-10-25
Changes: Data collection, Refinement description