3KGZ | pdb_00003kgz

Crystal structure of a cupin 2 conserved barrel domain protein from Rhodopseudomonas palustris

PDB DOI: https://doi.org/10.2210/pdb3KGZ/pdb

Classification: Structural Genomics, Unknown function
Organism(s): Rhodopseudomonas palustris TIE-1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-10-29 Released: 2009-11-24
Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Do, J., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.248 (Depositor), 0.255 (DCC)
R-Value Work:
0.199 (Depositor), 0.214 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3KGZ

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of a cupin 2 conserved barrel domain protein from Rhodopseudomonas palustris

Bonanno, J.B., Freeman, J., Bain, K.T., Do, J., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 35.37 kDa
Atom Count: 2,468
Modeled Residue Count: 290
Deposited Residue Count: 312
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cupin 2 conserved barrel domain protein	A, B	156	Rhodopseudomonas palustris TIE-1	Mutation(s): 0 Gene Names: Rpal_2463

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.248 (Depositor), 0.255 (DCC)
R-Value Work: 0.199 (Depositor), 0.214 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.854	α = 90
b = 80.382	β = 90
c = 110.081	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-11-24

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-11-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2018-11-21
Changes: Data collection, Structure summary
Version 1.4: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 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.