3PZI | pdb_00003pzi

Structure of the hyperthermostable endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 in complex with beta-D-glucose

PDB DOI: https://doi.org/10.2210/pdb3PZI/pdb

Classification: HYDROLASE
Organism(s): Thermotoga petrophila RKU-1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-12-14 Released: 2011-12-28
Deposition Author(s): Santos, C.R., Meza, A.N., Paiva, J.H., Silva, J.C., Ruller, R., Prade, R.A., Squina, F.M., Murakami, M.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.183 (Depositor), 0.175 (DCC)
R-Value Work:
0.140 (Depositor)
R-Value Observed:
0.142 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural characterization of a novel hyperthermostable endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1

Santos, C.R., Meza, A.N., Paiva, J.H., Silva, J.C., Ruller, R., Prade, R.A., Squina, F.M., Murakami, M.T.

To be published.

Macromolecule Content

Total Structure Weight: 44.39 kDa
Atom Count: 3,319
Modeled Residue Count: 357
Deposited Residue Count: 383
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannan endo-1,4-beta-mannosidase. Glycosyl Hydrolase family 5	A	383	Thermotoga petrophila RKU-1	Mutation(s): 0 Gene Names: Tpet_1542 EC: 3.2.1.78
UniProt
Find proteins for A5IMX7 (Thermotoga petrophila (strain ATCC BAA-488 / DSM 13995 / JCM 10881 / RKU-1)) Explore A5IMX7 Go to UniProtKB: A5IMX7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5IMX7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC Query on BGC 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]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.183 (Depositor), 0.175 (DCC)
R-Value Work: 0.140 (Depositor)
R-Value Observed: 0.142 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.43	α = 90
b = 83.234	β = 90
c = 91.916	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-12-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-12-28
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Structure summary

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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.