PDBsum entry 3d7a

Unknown function

PDB id: 3d7a

Contents

Protein chains

137 a.a. *

Waters ×176

* Residue conservation analysis

PDB id:

3d7a

Name:

Unknown function

Title:

Crystal structure of duf54 family protein ph1010 from hyperthermophilic archaea pyrococcus horikoshii ot3

Structure:

Upf0201 protein ph1010. Chain: a, b. Synonym: duf54 family protein. Engineered: yes

Source:

Pyrococcus horikoshii. Organism_taxid: 53953. Strain: ot3. Gene: ph1010. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.90Å R-factor: 0.240 R-free: 0.281

Authors:

M.Shirokane,K.I.Miyazono,Y.Sawano,M.Tanokura

Key ref:

K.Miyazono et al. (2009). Crystal structure of the DUF54 family protein PH1010 from hyperthermophilic archaea Pyrococcus horikoshii OT3. Proteins, 74, 256-260. PubMed id: 18831045 DOI: 10.1002/prot.22255

Date:

20-May-08 Release date: 09-Dec-08

Protein chains

O58738  (Y1010_PYRHO) -  UPF0201 protein PH1010 from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

Seq: 138 a.a.

Struc: 137 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1002/prot.22255

Proteins 74:256-260 (2009)

PubMed id: 18831045

Crystal structure of the DUF54 family protein PH1010 from hyperthermophilic archaea Pyrococcus horikoshii OT3.

K.Miyazono, M.Shirokane, Y.Sawano, M.Tanokura.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. The structure of PH1010. (A) Ribbon diagram of the monomer structure of PH1010 (Chain A). Color-coding runs from blue in the N-terminal region to red in the C-terminal region. Secondary structure assignments are labeled on the ribbon model. (B) The dimer structure of PH1010. One subunit is colored according to its secondary structure (helices, cyan; strands, pink) and the other is colored gray. The locations of Thr17 and the loop 4- 6 are indicated by red and blue circles, respectively. (C) Hydrogen-bond network observed in the dimerization interface. Residues forming the hydrogen-bond network are shown by a stick model. (D) The electrostatic potential diagram of the slightly twisted -sheet side of PH1010 and ribosomal protein L5. Positive and negative potentials are represented by blue and red, respectively. The maximum and the minimum values of the electrostatic potentials are ±5 kT/e, respectively.

Figure 2.
Figure 2. Comparison with other structures. (A) Superposition of PH1010 (cyan), 50S ribosomal protein L5 (gray), and SSO1042 (red). (B) Amino acid sequence alignment of PH1010 and other DUF54 family proteins: SSO1042 (PDB ID: 2NWU), MJ1564 (PDB ID: 2PZZ), Af2318 (PDB ID: 2OGK), and SSO0741 (PDB ID: 2NRQ). The secondary structure assignment for PH1010 is indicated by helices ( -helices) and arrows ( -strands). Residues forming the dimerization interface are indicated by an asterisk.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2009, 74, 256-260) copyright 2009.