2Z1K | pdb_00002z1k

Crystal Structure of Ttha1563 from Thermus thermophilus HB8

PDB DOI: https://doi.org/10.2210/pdb2Z1K/pdb

Classification: HYDROLASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-05-08 Released: 2008-05-13
Deposition Author(s): Niwa, H., Shimada, A., Matsunaga, E., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.236 (Depositor), 0.245 (DCC)
R-Value Work:
0.185 (Depositor), 0.198 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.3 of the entry. See complete history.

Literature

Crystal Structure of Ttha1563 from Thermus thermophilus HB8

Niwa, H., Shimada, A., Matsunaga, E., Kuramitsu, S., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 223.53 kDa
Atom Count: 16,422
Modeled Residue Count: 1,896
Deposited Residue Count: 1,900
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(Neo)pullulanase	A, B, C, D	475	Thermus thermophilus HB8	Mutation(s): 0 EC: 3.2.1.41
UniProt
Find proteins for Q5SI17 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SI17 Go to UniProtKB: Q5SI17
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SI17
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
Cycloheptakis-(1-4)-(alpha-D-glucopyranose)	E, G, I, K	7		N/A	Interactions Focus chain E Focus chain G Focus chain I Focus chain K Interactions & Density Focus chain E Focus chain G Focus chain I Focus chain K
Glycosylation Resources
GlyTouCan: G01435GL GlyCosmos: G01435GL

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	F, H, J, L	3		N/A	Interactions Focus chain F Focus chain H Focus chain J Focus chain L Interactions & Density Focus chain F Focus chain H Focus chain J Focus chain L
Glycosylation Resources
GlyTouCan: G96370VA GlyCosmos: G96370VA GlyGen: G96370VA

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [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

Biologically Interesting Molecules (External Reference)

2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900012 Query on PRD_900012	E, G, I, K	beta-cyclodextrin	Oligosaccharide / Drug delivery		Interactions Focus chain E Focus chain G Focus chain I Focus chain K Interactions & Density Focus chain E Focus chain G Focus chain I Focus chain K

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900009 Query on PRD_900009	F, H, J, L	alpha-maltotriose	Oligosaccharide / Nutrient		Interactions Focus chain F Focus chain H Focus chain J Focus chain L Interactions & Density Focus chain F Focus chain H Focus chain J Focus chain L

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.236 (Depositor), 0.245 (DCC)
R-Value Work: 0.185 (Depositor), 0.198 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.144	α = 90
b = 95.897	β = 94.4
c = 140.598	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-05-13

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-05-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2023-11-15
Changes: Data collection
Version 2.3: 2024-10-23
Changes: Structure summary