3P0B | pdb_00003p0b

Thermus thermophilus family GH57 branching enzyme: crystal structure, mechanism of action and products formed

PDB DOI: https://doi.org/10.2210/pdb3P0B/pdb

Classification: TRANSFERASE
Organism(s): Thermus thermophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-09-28 Released: 2010-10-20
Deposition Author(s): Pijning, T., Dijkstra, B.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.189 (Depositor), 0.189 (DCC)
R-Value Work:
0.169 (Depositor), 0.170 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Thermus thermophilus GLYCOSYL HYDROLASE FAMILY 57 branching enzyme: crystal structure, mechanism of action and products formed

Palomo-Reixach, M., Pijning, T., Booiman, T., Dobruchowska, J., van der Vlist, J., Kralj, S., Planas, A., Loos, K., Kamerling, J.P., Dijkstra, B.W., van der Maarel, M.J.E.C., Dijkhuizen, L., Leemhuis, H.

To be published.

Macromolecule Content

Total Structure Weight: 61.52 kDa
Atom Count: 4,987
Modeled Residue Count: 511
Deposited Residue Count: 540
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TT1467 protein	A	540	Thermus thermophilus	Mutation(s): 0 Gene Names: tthHB8IM EC: 2.4.1.18
UniProt
Find proteins for Q5SH28 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SH28 Go to UniProtKB: Q5SH28
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SH28
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.189 (Depositor), 0.189 (DCC)
R-Value Work: 0.169 (Depositor), 0.170 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.532	α = 90
b = 119.532	β = 90
c = 74.097	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-10-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-10-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.