6C4Q

1.16 Angstrom Resolution Crystal Structure of Acyl Carrier Protein Domain (residues 1-100) of Polyketide Synthase Pks13 from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb6C4Q/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-01-12 Released: 2018-01-24
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Kiryukhina, O., Grimshaw, S., Kwon, K., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free: 0.145
R-Value Work: 0.130
R-Value Observed: 0.130

wwPDB Validation 3D Report Full Report

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

Literature

1.16 Angstrom Resolution Crystal Structure of Acyl Carrier Protein Domain (residues 1-100) of Polyketide Synthase Pks13 from Mycobacterium tuberculosis.

Minasov, G., Shuvalova, L., Dubrovska, I., Kiryukhina, O., Grimshaw, S., Kwon, K., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 11.34 kDa
Atom Count: 868
Modelled Residue Count: 85
Deposited Residue Count: 103
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyketide synthase Pks13	A	103	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: pks13, Rv3800c EC: 2.3.1
UniProt
Find proteins for I6X8D2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6X8D2 Go to UniProtKB: I6X8D2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I6X8D2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free: 0.145
R-Value Work: 0.130
R-Value Observed: 0.130
Space Group: P 4₃ 2₁ 2
Diffraction Data: https://doi.org/10.18430/m36c4q

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.889	α = 90
b = 51.889	β = 90
c = 74.427	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-01-24

Deposition Author(s):

Satchell, K.J.F.

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2018-01-24
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Structure summary

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.