4HVM

Crystal structure of tallysomycin biosynthesis protein TlmII

PDB DOI: https://doi.org/10.2210/pdb4HVM/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Streptoalloteichus hindustanus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-11-06 Released: 2012-11-21
Deposition Author(s): Chang, C., Bigelow, L., Bearden, J., Babnigg, G., Bingman, C.A., Yennamalli, R., Lohman, J., Ma, M., Shen, B., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.232 (Depositor), 0.246 (DCC)
R-Value Work:
0.182 (Depositor), 0.195 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of tallysomycin biosynthesis protein TlmII

Chang, C., Bigelow, L., Bearden, J., Babnigg, G., Bingman, C.A., Yennamalli, R., Lohman, J., Ma, M., Shen, B., Phillips Jr., G.N., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 216.85 kDa
Atom Count: 12,790
Modelled Residue Count: 1,627
Deposited Residue Count: 1,972
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TlmII	A, B, C, D	493	Streptoalloteichus hindustanus	Mutation(s): 0 Gene Names: tlmII
UniProt
Find proteins for A4KUC0 (Streptoalloteichus hindustanus) Explore A4KUC0 Go to UniProtKB: A4KUC0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4KUC0
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth D]	E [auth A], F [auth A], G [auth B], H [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.232 (Depositor), 0.246 (DCC)
R-Value Work: 0.182 (Depositor), 0.195 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.799	α = 90
b = 128.015	β = 90
c = 129.307	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXDE	phasing
RESOLVE	model building
ARP/wARP	model building
COO	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing
COO	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-11-21

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Revision History (Full details and data files)

Version 1.0: 2012-11-21
Type: Initial release
Version 1.1: 2013-09-18
Changes: Structure summary
Version 1.2: 2014-04-16
Changes: Experimental preparation
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary