3VYV

Crystal structure of subtilisin NAT at 1.36

PDB DOI: https://doi.org/10.2210/pdb3VYV/pdb

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

Deposited: 2012-10-03 Released: 2013-10-09
Deposition Author(s): Ushijima, H., Fuchita, N., Kajiwara, T., Motoshima, H., Ueno, G., Watanabe, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.36 Å
R-Value Free: 0.176
R-Value Work: 0.146
R-Value Observed: 0.148

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of subtilisin NAT at 1.36

Watanabe, K.

To be published.

Macromolecule Content

Total Structure Weight: 56.14 kDa
Atom Count: 4,350
Modelled Residue Count: 550
Deposited Residue Count: 550
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35835
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A]	C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B]	E [auth A], F [auth A], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEB Query on SEB	A, B	L-PEPTIDE LINKING	C₁₀ H₁₃ N O₅ S		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.36 Å
R-Value Free: 0.176
R-Value Work: 0.146
R-Value Observed: 0.148
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.682	α = 90
b = 80.039	β = 90
c = 87.449	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
d*TREK	data reduction
CrystalClear	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-10-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-09
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3VYV

Crystal structure of subtilisin NAT at 1.36

Crystal structure of subtilisin NAT at 1.36

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)