3NI7 | pdb_00003ni7

Crystal structure of the TetR transcriptional regulator from Nitrosomonas europaea ATCC 19718

PDB DOI: https://doi.org/10.2210/pdb3NI7/pdb

Classification: TRANSCRIPTION REGULATOR
Organism(s): Nitrosomonas europaea
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-06-15 Released: 2010-08-11
Deposition Author(s): Knapik, A., Chruszcz, M., Cymborowski, M., Xu, X., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.78 Å
R-Value Free:
0.279 (Depositor), 0.266 (DCC)
R-Value Work:
0.249 (Depositor), 0.255 (DCC)
R-Value Observed:
0.250 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3NI7

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of the TetR transcriptional regulator from Nitrosomonas europaea ATCC 19718

Knapik, A., Chruszcz, M., Cymborowski, M., Xu, X., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 51.21 kDa
Atom Count: 2,735
Modeled Residue Count: 347
Deposited Residue Count: 426
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterial regulatory proteins, TetR family	A, B	213	Nitrosomonas europaea	Mutation(s): 0 Gene Names: NE0300
UniProt
Find proteins for Q82XH4 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)) Explore Q82XH4 Go to UniProtKB: Q82XH4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q82XH4
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 2.78 Å
R-Value Free: 0.279 (Depositor), 0.266 (DCC)
R-Value Work: 0.249 (Depositor), 0.255 (DCC)
R-Value Observed: 0.250 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.222	α = 90
b = 75.378	β = 90
c = 98.079	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
ARP/wARP	model building
BUCCANEER	model building
REFMAC	refinement
Coot	model building
HKL-2000	data reduction
HKL-2000	data scaling
DM	phasing
RESOLVE	phasing
BUCCANEER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-08-11

Deposition Author(s):

Cymborowski, M.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-08-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-06-20
Changes: Database references
Version 1.3: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-10-30
Changes: Data collection, 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.