2FFI | pdb_00002ffi

Crystal Structure of Putative 2-Pyrone-4,6-Dicarboxylic Acid Hydrolase from Pseudomonas putida, Northeast Structural Genomics Target PpR23.

PDB DOI: https://doi.org/10.2210/pdb2FFI/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Pseudomonas putida KT2440
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-12-19 Released: 2005-12-27
Deposition Author(s): Forouhar, F., Su, M., Jayaraman, S., Conover, K., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free:
0.287 (Depositor), 0.298 (DCC)
R-Value Work:
0.228 (Depositor), 0.249 (DCC)
R-Value Observed:
0.228 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2FFI

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Putative 2-Pyrone-4,6-Dicarboxylic Acid Hydrolase from Pseudomonas putida, Northeast Structural Genomics Target PpR23.

Forouhar, F., Su, M., Jayaraman, S., Conover, K., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

To be published.

Macromolecule Content

Total Structure Weight: 65.05 kDa
Atom Count: 4,331
Modeled Residue Count: 546
Deposited Residue Count: 576
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-pyrone-4,6-dicarboxylic acid hydrolase, putative	A, B	288	Pseudomonas putida KT2440	Mutation(s): 7 Gene Names: PP1699 EC: 3.1.1.57
UniProt
Find proteins for Q88M75 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88M75 Go to UniProtKB: Q88M75
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q88M75
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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: 2.61 Å
R-Value Free: 0.287 (Depositor), 0.298 (DCC)
R-Value Work: 0.228 (Depositor), 0.249 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.392	α = 80.86
b = 46.289	β = 76.86
c = 64.078	γ = 80.61

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
XTALVIEW	refinement

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-12-27

Deposition Author(s):

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2005-12-27
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2024-10-09
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.