1Y9Z | pdb_00001y9z

Crystal Structure of Psychrophilic Subtilisin-like Serine Protease from Antarctic Psychrotroph Pseudoalteromonas sp. AS-11 at 0.14 nm resolution

PDB DOI: https://doi.org/10.2210/pdb1Y9Z/pdb

Classification: HYDROLASE
Organism(s): Pseudoalteromonas sp. AS-11
Mutation(s): No

Deposited: 2004-12-16 Released: 2006-03-21
Deposition Author(s): Dong, D., Watanabe, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.207 (Depositor), 0.200 (DCC)
R-Value Work:
0.197 (Depositor), 0.190 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Psychrophilic Subtilisin-like Serine Protease from Antarctic Psychrotroph Pseudoalteromonas sp. AS-11 at 0.14 nm resolution

Dong, D., Watanabe, K.

To be published.

Macromolecule Content

Total Structure Weight: 91.21 kDa
Atom Count: 6,853
Modeled Residue Count: 871
Deposited Residue Count: 882
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alkaline serine protease	A, B	441	Pseudoalteromonas sp. AS-11	Mutation(s): 0 EC: 3.4.21
UniProt
Find proteins for Q65Z69 (Pseudoalteromonas sp. AS-11) Explore Q65Z69 Go to UniProtKB: Q65Z69
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q65Z69
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PMS Query on PMS Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain H [auth A]	H [auth A], O [auth B]	phenylmethanesulfonic acid C₇ H₈ O₃ S NIXKBAZVOQAHGC-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain O [auth B]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain G [auth A]	G [auth A], N [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain N [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], L [auth B], M [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.207 (Depositor), 0.200 (DCC)
R-Value Work: 0.197 (Depositor), 0.190 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.09	α = 90
b = 138.32	β = 97.49
c = 64.79	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-03-21

Deposition Author(s):

Dong, D.

Watanabe, K.

Revision History (Full details and data files)

Version 1.0: 2006-03-21
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-16
Changes: Structure summary

1Y9Z | pdb_00001y9z

Crystal Structure of Psychrophilic Subtilisin-like Serine Protease from Antarctic Psychrotroph Pseudoalteromonas sp. AS-11 at 0.14 nm resolution

Literature

Crystal Structure of Psychrophilic Subtilisin-like Serine Protease from Antarctic Psychrotroph Pseudoalteromonas sp. AS-11 at 0.14 nm resolution

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)