2RFR | pdb_00002rfr

Crystal structure of an ntf2-like protein with a cystatin-like fold (saro_3722) from novosphingobium aromaticivorans dsm at 1.16 A resolution

PDB DOI: https://doi.org/10.2210/pdb2RFR/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Novosphingobium aromaticivorans DSM 12444
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-10-01 Released: 2007-10-16
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free:
0.172 (Depositor), 0.180 (DCC)
R-Value Work:
0.141 (Depositor), 0.150 (DCC)
R-Value Observed:
0.142 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of uncharacterized protein (YP_001166107.1) from Novosphingobium aromaticivorans DSM 12444 at 1.16 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 16.89 kDa
Atom Count: 1,549
Modeled Residue Count: 154
Deposited Residue Count: 155
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	155	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 0 Gene Names: YP_001166107.1, Saro_3722
UniProt
Find proteins for A4XF70 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore A4XF70 Go to UniProtKB: A4XF70
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4XF70
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free: 0.172 (Depositor), 0.180 (DCC)
R-Value Work: 0.141 (Depositor), 0.150 (DCC)
R-Value Observed: 0.142 (Depositor)

Diffraction Data: https://doi.org/10.18430/M32RFR

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.135	α = 90
b = 63.135	β = 90
c = 75.118	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-10-16

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-10-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-01-25
Changes: Database references
Version 1.5: 2024-11-13
Changes: Data collection, Structure summary

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.