3M7T | pdb_00003m7t

Crystal Structure of Alpha-Lytic Protease SB2+3 E8A/R105S Mutant

PDB DOI: https://doi.org/10.2210/pdb3M7T/pdb

Classification: HYDROLASE
Organism(s): Lysobacter enzymogenes
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-03-17 Released: 2011-02-09
Deposition Author(s): Agard, D.A., Erciyas Bailey, F.P., Waddling, C.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.202 (Depositor), 0.197 (DCC)
R-Value Work:
0.136 (Depositor), 0.134 (DCC)
R-Value Observed:
0.138 (Depositor)

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

Quantifying protein unfolding cooperativity with acid sensitive probes: Interdomain salt bridge contributions to unfolding cooperativity are combined efficiently in alpha-Lytic Protease

Erciyas Bailey, F.P., Waddling, C.A., Agard, D.A.

To be published.

Macromolecule Content

Total Structure Weight: 20.32 kDa
Atom Count: 1,913
Modeled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-lytic protease	A	198	Lysobacter enzymogenes	Mutation(s): 2 Gene Names: alpha-LP, Lysobacter EC: 3.4.21.12
UniProt
Find proteins for P00778 (Lysobacter enzymogenes) Explore P00778 Go to UniProtKB: P00778
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00778
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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: 1.55 Å
R-Value Free: 0.202 (Depositor), 0.197 (DCC)
R-Value Work: 0.136 (Depositor), 0.134 (DCC)
R-Value Observed: 0.138 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.015	α = 90
b = 66.015	β = 90
c = 79.749	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-02-09

Deposition Author(s):

Erciyas Bailey, F.P.

Revision History (Full details and data files)

Version 1.0: 2011-02-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-06
Changes: Database references, Derived calculations
Version 1.3: 2023-09-06
Changes: Data collection, Refinement description
Version 1.4: 2024-11-20
Changes: 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.