3MJI | pdb_00003mji

Activation of catalytic cysteine without a base in a Mutant Penicillin Acylase Precursor

PDB DOI: https://doi.org/10.2210/pdb3MJI/pdb

Classification: HYDROLASE
Organism(s): Lysinibacillus sphaericus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-04-12 Released: 2011-07-20
Deposition Author(s): Pathak, M.C., Suresh, C.G., Dodson, G.G., Murshudov, G.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.211 (Depositor), 0.208 (DCC)
R-Value Work:
0.166 (Depositor), 0.172 (DCC)
R-Value Observed:
0.168 (Depositor)

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

Literature

Activation of catalytic cysteine without a base in a Mutant Penicillin Acylase Precursor

Pathak, M.C., Suresh, C.G., Dodson, G.G., Murshudov, G.N.

To be published.

Macromolecule Content

Total Structure Weight: 150.12 kDa
Atom Count: 10,729
Modeled Residue Count: 1,334
Deposited Residue Count: 1,352
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin acylase	A, B, C, D	338	Lysinibacillus sphaericus	Mutation(s): 0 EC: 3.5.1.11
UniProt
Find proteins for P12256 (Lysinibacillus sphaericus) Explore P12256 Go to UniProtKB: P12256
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12256
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.211 (Depositor), 0.208 (DCC)
R-Value Work: 0.166 (Depositor), 0.172 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.642	α = 90
b = 90.089	β = 102.13
c = 102.269	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-07-20

Deposition Author(s):

Murshudov, G.N.

Revision History (Full details and data files)

Version 1.0: 2011-07-20
Type: Initial release
Version 1.1: 2018-01-24
Changes: Structure summary
Version 1.2: 2024-02-21
Changes: Data collection, Database references

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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.