3DA7: Barnase circular permutant

A conformationally strained, circular permutant of barnase. Determined by X-ray diffraction at 2.25 Å resolution. Released 14 Apr 2009.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: Bacillus amyloliquefaciens
Chains: 8
Atoms: 6,544
Mol. weight: 91.42 kDa
Released: 14 Apr 2009

Explore 3DA7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3DA7 contains 32 α-helices and 42 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	16	1	2
β-strand	22-26	5	1
β-strand	31-34	4	1
β-strand	42-43	2	1
α-helix	52-63	12
β-strand	70-71	2	3
α-helix	73-78	6
β-strand	87	1	2
α-helix	88-91	4
β-strand	96-97	2	3
β-strand	98-102	5	1
α-helix	110-111	2

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	4
β-strand	22-26	5	4
β-strand	31-34	4	4
β-strand	42-43	2	4
α-helix	55-63	9
β-strand	70-71	2	5
α-helix	73-76	4
α-helix	88-91	4
β-strand	96-97	2	5
β-strand	98-102	5	4

Chain C: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	6
α-helix	14-25	12
α-helix	35-44	10
β-strand	50-55	6	6
α-helix	57-62	6
α-helix	67-80	14
β-strand	85-89	5	6

Chain D: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	7
α-helix	14-24	11
α-helix	35-44	10
β-strand	50-55	6	7
α-helix	57-62	6
α-helix	68-80	13
β-strand	85-89	5	7

Chain E: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	8
β-strand	22-26	5	8
β-strand	31-34	4	8
β-strand	42-43	2	8
α-helix	55-63	9
β-strand	70-71	2	9
α-helix	73-77	5
α-helix	83-85	3
α-helix	88-91	4
β-strand	96-97	2	9
β-strand	98-102	5	8

Chain F: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	10
α-helix	8-10	3
α-helix	14-24	11
α-helix	35-43	9
β-strand	50-55	6	10
α-helix	57-63	7
α-helix	67-80	14
β-strand	85-89	5	10

Chain G: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	11
β-strand	22-26	5	11
β-strand	31-34	4	11
β-strand	42-44	3	11
α-helix	57-63	7
β-strand	70-71	2	12
α-helix	73-78	6
α-helix	88-91	4
β-strand	96-97	2	12
β-strand	98-102	5	11

Chain H: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
α-helix	8-10	3
α-helix	14-24	11
α-helix	35-44	10
β-strand	50-55	6	7
α-helix	57-62	6
α-helix	67-81	15
β-strand	85-89	5	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Barnase circular permutant	A, B, E, G	protein	111	Bacillus amyloliquefaciens	P00648 (AlphaFold model)
Barstar	C, D, F, H	protein	90	Bacillus amyloliquefaciens	P11540 (AlphaFold model)

Sequence of entity 1 (A, B, E, G), FASTA

>3DA7_1 Barnase circular permutant (chains A, B, E, G)
SGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIRCAQVINTFDGVADYLQ
TYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGK

Sequence of entity 2 (C, D, F, H), FASTA

>3DA7_2 Barstar (chains C, D, F, H)
MKKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDCLTGWVEYPLVLEWRQFEQS
KQLTENGAESVLQVFREAKAEGCDITIILS

Primary citation

Structural and thermodynamic analysis of a conformationally strained circular permutant of barnase. Butler, J.S., Mitrea, D.M., Mitrousis, G. et al. Biochemistry (2009) 48:3497-3507. DOI 10.1021/bi900039e · PubMed

Other PDB entries of the same protein (UniProt P00648 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6PQK 1.2 Å, Cryogenic crystal structure of barnase A43C/S80C bound to barstar C40A/S59C/A67C/C82A
2C4B 1.3 Å, Inhibitor cystine knot protein McoEeTI fused to the catalytically inactive barnase…
1A2P 1.5 Å, Barnase wildtype structure at 1.5 Å resolution
2ZA4 1.58 Å, Crystal Structural Analysis of Barnase-barstar Complex
1B20 1.7 Å, Deletion of a buried salt-bridge in barnase
1BRN 1.76 Å, Subsite binding in an RNase: structure of a barnase-tetranucleotide complex at 1.76 Å…
1B2X 1.8 Å, Barnase wildtype structure at PH 7.5 from a cryo_cooled crystal at 100K
1B2S 1.82 Å, Structural response to mutation at a protein-protein interface
1BRI 1.9 Å, Barnase mutant with ile 76 replaced by ala
1RNB 1.9 Å, Crystal structure of a barnase-d(*gp*c) complex at 1.9 Å resolution
1X1Y 1.9 Å, Water-mediate interaction at aprotein-protein interface
3KCH 1.94 Å, Baranase crosslinked by glutaraldehyde

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