3GWB | pdb_00003gwb

Crystal structure of peptidase M16 inactive domain from Pseudomonas fluorescens. Northeast Structural Genomics target PlR293L

PDB DOI: https://doi.org/10.2210/pdb3GWB/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas protegens Pf-5
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-03-31 Released: 2009-05-12
Deposition Author(s): Seetharaman, J., Chen, Y., Fang, F., Xiao, R., Everett, J.K., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.240 (Depositor), 0.251 (DCC)
R-Value Work:
0.204 (Depositor)
R-Value Observed:
0.204 (Depositor)

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

Literature

Crystal structure of peptidase M16 inactive domain from Pseudomonas fluorescens. Northeast Structural Genomics target PlR293L

Seetharaman, J., Chen, Y., Fang, F., Xiao, R., Everett, J.K., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 94.18 kDa
Atom Count: 6,636
Modeled Residue Count: 824
Deposited Residue Count: 868
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase M16 inactive domain family protein	A, B	434	Pseudomonas protegens Pf-5	Mutation(s): 0 Gene Names: PFL_5859 EC: 3.4.24
UniProt
Find proteins for Q4K4B6 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)) Explore Q4K4B6 Go to UniProtKB: Q4K4B6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4K4B6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.240 (Depositor), 0.251 (DCC)
R-Value Work: 0.204 (Depositor)
R-Value Observed: 0.204 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.673	α = 90
b = 64.841	β = 96.39
c = 114.972	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-05-12

Deposition Author(s):

Seetharaman, J.

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-05-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, 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.