1DUI | pdb_00001dui

Subtilisin BPN' from Bacillus amyloliquefaciens, crystal growth mutant

PDB DOI: https://doi.org/10.2210/pdb1DUI/pdb

Classification: HYDROLASE
Organism(s): Bacillus amyloliquefaciens
Expression System: Bacillus amyloliquefaciens
Mutation(s): Yes

Deposited: 2000-01-17 Released: 2000-01-28
Deposition Author(s): Pan, Q., Gallagher, D.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.283 (Depositor)
R-Value Work:
0.200 (Depositor), 0.189 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Probing Protein Interaction Chemistry Through Crystal Growth: Structure, Mutation, and Mechanism in Subtilisin s88

Pan, Q., Gallagher, D.T.

(2000) J Cryst Growth 212: 555-563

Macromolecule Content

Total Structure Weight: 26.84 kDa
Atom Count: 1,983
Modeled Residue Count: 266
Deposited Residue Count: 266
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (SUBTILISIN BPN')	A	266	Bacillus amyloliquefaciens	Mutation(s): 10 EC: 3.4.21.62
UniProt
Find proteins for P00782 (Bacillus amyloliquefaciens) Explore P00782 Go to UniProtKB: P00782
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00782
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DFP Query on DFP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DIISOPROPYL PHOSPHONATE C₆ H₁₅ O₃ P BLKXLEPPVDUHBY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.283 (Depositor)
R-Value Work: 0.200 (Depositor), 0.189 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.289	α = 90
b = 58.527	β = 90
c = 85.168	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
TNT	refinement
TNT	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2000-01-28

Deposition Author(s):

Gallagher, D.T.

Revision History (Full details and data files)

Version 1.0: 2000-01-28
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-11-03
Changes: Database references, Derived calculations
Version 1.4: 2024-11-13
Changes: Data collection, 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.