4M1A | pdb_00004m1a

Crystal structure of a Domain of unknown function (DUF1904) from Sebaldella termitidis ATCC 33386

PDB DOI: https://doi.org/10.2210/pdb4M1A/pdb

Classification: Structural Genomics, Unknown Function
Organism(s): Sebaldella termitidis ATCC 33386
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-08-02 Released: 2013-08-14
Deposition Author(s): Kumaran, D., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Al Obaidi, N., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.206 (Depositor), 0.216 (DCC)
R-Value Work:
0.176 (Depositor), 0.189 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a Domain of unknown function (DUF1904) from Sebaldellatermitidis ATCC 33386

Kumaran, D., Almo, S.C., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 30.21 kDa
Atom Count: 1,893
Modeled Residue Count: 216
Deposited Residue Count: 252
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B	126	Sebaldella termitidis ATCC 33386	Mutation(s): 0 Gene Names: Sterm_0053
UniProt
Find proteins for D1AJN4 (Sebaldella termitidis (strain ATCC 33386 / NCTC 11300)) Explore D1AJN4 Go to UniProtKB: D1AJN4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D1AJN4
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: 1.90 Å
R-Value Free: 0.206 (Depositor), 0.216 (DCC)
R-Value Work: 0.176 (Depositor), 0.189 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.283	α = 90
b = 90.283	β = 90
c = 37.099	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHELXE	model building
ARP/wARP	model building
Coot	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-08-14

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-08-14
Type: Initial release
Version 1.1: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary