7BRF

Structure of NADH complex of Thermotoga maritima alpha-glucuronidase at 2.15 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb7BRF/pdb

Classification: HYDROLASE
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-03-28 Released: 2021-03-31
Deposition Author(s): Manoj, N., Mohapatra, S.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.215
R-Value Work: 0.178
R-Value Observed: 0.180

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Structure of NADH complex of Thermotoga maritima alpha-glucuronidase at 2.15 Angstrom resolution

Manoj, N., Mohapatra, S.B.

To be published.

Macromolecule Content

Total Structure Weight: 57.58 kDa
Atom Count: 4,017
Modelled Residue Count: 469
Deposited Residue Count: 483
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-glucosidase, putative	A	483	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: TM_0752
UniProt
Find proteins for Q9WZL1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZL1 Go to UniProtKB: Q9WZL1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WZL1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI (Subject of Investigation/LOI) Query on NAI Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.215
R-Value Work: 0.178
R-Value Observed: 0.180
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.33	α = 90
b = 81.06	β = 103.02
c = 88.76	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-03-31

Deposition Author(s):

Mohapatra, S.B.

Revision History (Full details and data files)

Version 1.0: 2021-03-31
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description

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 R01GM133198.