3OCR | pdb_00003ocr

Crystal structure of aldolase II superfamily protein from Pseudomonas syringae

PDB DOI: https://doi.org/10.2210/pdb3OCR/pdb

Classification: LYASE
Organism(s): Pseudomonas savastanoi pv. phaseolicola 1448A
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-08-10 Released: 2010-08-25
Deposition Author(s): Chang, C., Kagan, O., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.240 (Depositor), 0.229 (DCC)
R-Value Work:
0.183 (Depositor)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of aldolase II superfamily protein from Pseudomonas syringae

Chang, C., Kagan, O., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 59.57 kDa
Atom Count: 4,405
Modeled Residue Count: 499
Deposited Residue Count: 546
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Class II aldolase/adducin domain protein	A, B	273	Pseudomonas savastanoi pv. phaseolicola 1448A	Mutation(s): 0 Gene Names: PSPPH_2884
UniProt
Find proteins for Q48HR6 (Pseudomonas savastanoi pv. phaseolicola (strain 1448A / Race 6)) Explore Q48HR6 Go to UniProtKB: Q48HR6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q48HR6
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 C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [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: 1.95 Å
R-Value Free: 0.240 (Depositor), 0.229 (DCC)
R-Value Work: 0.183 (Depositor)
R-Value Observed: 0.186 (Depositor)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.407	α = 90
b = 74.407	β = 90
c = 179.909	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
Coot	model building
ARP/wARP	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-08-25

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-08-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
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.