7D41 | pdb_00007d41

Crystal structure of type III polyketide synthase from Mycobacterium marinum - P 21 21 21 Space group

PDB DOI: https://doi.org/10.2210/pdb7D41/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium marinum M
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-09-21 Released: 2022-03-23
Deposition Author(s): Pratap, S., Kant, A., Saxena, P., Krishnan, V.
Funding Organization(s): Department of Science & Technology (DST, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free:
0.258 (Depositor), 0.260 (DCC)
R-Value Work:
0.204 (Depositor), 0.210 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

crystal structure of type III polyketide synthase from Mycobacterium marinum

Pratap, S., Kant, A., Saxena, P., Krishnan, V.

To be published.

Macromolecule Content

Total Structure Weight: 89.47 kDa
Atom Count: 5,434
Modeled Residue Count: 732
Deposited Residue Count: 826
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chalcone synthase-like protein	A [auth B]	413	Mycobacterium marinum M	Mutation(s): 0 Gene Names: MMAR_2190
UniProt
Find proteins for B2HNE1 (Mycobacterium marinum (strain ATCC BAA-535 / M)) Explore B2HNE1 Go to UniProtKB: B2HNE1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B2HNE1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chalcone/stilbene synthase	B [auth A]	413	Mycobacterium marinum M	Mutation(s): 0 Gene Names: MMAR_2190
UniProt
Find proteins for B2HNE1 (Mycobacterium marinum (strain ATCC BAA-535 / M)) Explore B2HNE1 Go to UniProtKB: B2HNE1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B2HNE1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OCA (Subject of Investigation/LOI) Query on OCA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth B]	C [auth B], D [auth A]	OCTANOIC ACID (CAPRYLIC ACID) C₈ H₁₆ O₂ WWZKQHOCKIZLMA-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MCS Query on MCS	B [auth A]	L-PEPTIDE LINKING	C₆ H₉ N O₅ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.258 (Depositor), 0.260 (DCC)
R-Value Work: 0.204 (Depositor), 0.210 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.732	α = 90
b = 99.518	β = 90
c = 126.707	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
SHELXDE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-03-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Science & Technology (DST, India)	India	CRG/2018/002229

Revision History (Full details and data files)

Version 1.0: 2022-03-23
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Derived calculations, 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.