3ERM | pdb_00003erm

The crystal structure of a conserved protein with unknown function from Pseudomonas syringae pv. tomato str. DC3000

PDB DOI: https://doi.org/10.2210/pdb3ERM/pdb

Classification: structural genomics, unknown function
Organism(s): Pseudomonas syringae pv. tomato
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-10-02 Released: 2008-10-21
Deposition Author(s): Tan, K., Zhou, M., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.269 (Depositor), 0.270 (DCC)
R-Value Work:
0.214 (Depositor), 0.215 (DCC)
R-Value Observed:
0.217 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of a conserved protein with unknown function from Pseudomonas syringae pv. tomato str. DC3000

Tan, K., Zhou, M., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 50.64 kDa
Atom Count: 2,449
Modeled Residue Count: 318
Deposited Residue Count: 455
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized conserved protein	A, B, C, D, E	91	Pseudomonas syringae pv. tomato	Mutation(s): 0 Gene Names: Pseudomonas syringae pv. tomato, PSPTO1197, PSPTO_1197
UniProt
Find proteins for Q887T9 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q887T9 Go to UniProtKB: Q887T9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q887T9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.269 (Depositor), 0.270 (DCC)
R-Value Work: 0.214 (Depositor), 0.215 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.971	α = 90
b = 74.971	β = 90
c = 213.784	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
RESOLVE	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-10-21

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-10-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.3: 2024-11-13
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.