5GL8 | pdb_00005gl8

The crystal structure of Nattokinase fragments

PDB DOI: https://doi.org/10.2210/pdb5GL8/pdb

Classification: HYDROLASE
Organism(s): Bacillus subtilis subsp. natto
Mutation(s): No

Deposited: 2016-07-10 Released: 2017-10-25
Deposition Author(s): Liu, W.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.291 (Depositor), 0.305 (DCC)
R-Value Work:
0.231 (Depositor), 0.244 (DCC)
R-Value Observed:
0.234 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5GL8

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

Literature

unpublished

Ren, Y., Pan, X., Lyu, Q., Liu, W.

To be published.

Macromolecule Content

Total Structure Weight: 55.54 kDa
Atom Count: 4,747
Modeled Residue Count: 550
Deposited Residue Count: 550
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Subtilisin NAT	A, B	275	Bacillus subtilis subsp. natto	Mutation(s): 0 EC: 3.4.21.62
UniProt
Find proteins for P35835 (Bacillus subtilis subsp. natto) Explore P35835 Go to UniProtKB: P35835
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35835
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth B]	C [auth B], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.291 (Depositor), 0.305 (DCC)
R-Value Work: 0.231 (Depositor), 0.244 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.284	α = 90
b = 73.959	β = 97.47
c = 67.811	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-10-25

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	8130268

Revision History (Full details and data files)

Version 1.0: 2017-10-25
Type: Initial release
Version 1.1: 2018-07-18
Changes: Data collection, Database references
Version 1.2: 2023-11-08
Changes: Data collection, Database references, 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.