3NA2 | pdb_00003na2

Crystal Structure of Protein of Unknown Function from Mine Drainage Metagenome Leptospirillum rubarum

PDB DOI: https://doi.org/10.2210/pdb3NA2/pdb

Classification: Structural Genomics, Unknown function
Organism(s): Leptospirillum rubarum
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2010-05-31 Released: 2010-07-28
Deposition Author(s): Kim, Y., Xu, X., Cui, H., Chin, S., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.248 (Depositor), 0.243 (DCC)
R-Value Work:
0.186 (Depositor), 0.182 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3NA2

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

Literature

Crsystal Structure of Protein of Unknown Function from Mine Drainage Metagenome Leptospirillum rubarum

Kim, Y., Xu, X., Cui, H., Chin, S., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 79.05 kDa
Atom Count: 4,516
Modeled Residue Count: 537
Deposited Residue Count: 688
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D	172	Leptospirillum rubarum	Mutation(s): 0 Gene Names: UBAL2_80620259

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth D]	F [auth A], H [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth D]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain E [auth A] MOL2 format, chain G [auth D] MOL2 format, chain E [auth A] mmCIF format, chain G [auth D] mmCIF format, chain E [auth A]	E [auth A], G [auth D]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.248 (Depositor), 0.243 (DCC)
R-Value Work: 0.186 (Depositor), 0.182 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.367	α = 90
b = 115.047	β = 90
c = 73.596	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
RESOLVE	model building
SOLVE	phasing
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-07-28

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-07-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-30
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.