1B2X - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   BARNASE WILDTYPE STRUCTURE AT PH 7.5 FROM A CRYO_COOLED CRYSTAL AT 100K

Authors :   P. Harrison, C. K. Vaughan, A. M. Buckle, A. R. Fersht

Date :   03 Dec 98 (Deposition) - 09 Dec 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Microbial Ribonuclease, Alpha/Beta Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. K. Vaughan, P. Harryson, A. M. Buckle, A. R. Fersht
A Structural Double-Mutant Cycle: Estimating The Strength Of A Buried Salt Bridge In Barnase.
Acta Crystallogr. , Sect. D V. 58 591 2002
PubMed-ID: 11914482 | Reference-DOI: 10.1107/S0907444902001567
(for further references see the PDB file header)

Molecule 1 - PROTEIN (BARNASE)
	Cellular Location	:	EXTRACELLULAR
	Chains	:	A, B, C
	EC Number	:	3.1.27.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMT410
	Expression System Taxid	:	562
	Expression System Vector	:	PUC19
	Organism Scientific	:	BACILLUS AMYLOLIQUEFACIENS
	Organism Taxid	:	1390

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:133 , HIS C:18 , GLU C:60 , LYS C:62	BINDING SITE FOR RESIDUE ZN C 384

(no "SS Bond" information available for 1B2X)

(no "Cis Peptide Bond" information available for 1B2X)

(no "SAP(SNP)/Variant" information available for 1B2X)

(no "PROSITE Motif" information available for 1B2X)

(no "Exon" information available for 1B2X)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:109
 aligned with RNBR_BACAM | P00648 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:109
                                    58        68        78        88        98       108       118       128       138       148         
           RNBR_BACAM    49 QVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 157
               SCOP domains d1b2xa_ A: Barnase                                                                                            SCOP domains
               CATH domains 1b2xA00 A:2-110  [code=3.10.450.30, no name defined]                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh.........hhhhhhh...hhh..hhhh......eeeee..............eeeee...........eeeee....eeee.......eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1b2x A   2 QVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 110
                                    11        21        31        41        51        61        71        81        91       101

Chain B from PDB  Type:PROTEIN  Length:108
 aligned with RNBR_BACAM | P00648 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:108
                                    59        69        79        89        99       109       119       129       139       149        
           RNBR_BACAM    50 VINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 157
               SCOP domains d1b2xb_ B: Barnase                                                                                           SCOP domains
               CATH domains 1b2xB00 B:3-110  [code=3.10.450.30, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhh.........hhhhhhh...hhh..hhhh......eeeee..............eeeee...........eeeee....eeee.......eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1b2x B   3 VINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 110
                                    12        22        32        42        52        62        72        82        92       102

Chain C from PDB  Type:PROTEIN  Length:108
 aligned with RNBR_BACAM | P00648 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:108
                                    59        69        79        89        99       109       119       129       139       149        
           RNBR_BACAM    50 VINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 157
               SCOP domains d1b2xc_ C: Barnase                                                                                           SCOP domains
               CATH domains 1b2xC00 C:3-110  [code=3.10.450.30, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhh.........hhhhhh....hhh..hhhh......eeeee..............eeeee...........eeeee....eeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1b2x C   3 VINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR 110
                                    12        22        32        42        52        62        72        82        92       102

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Microbial ribonucleases (174)

Superfamily: Microbial ribonucleases (174)

Family: Bacterial ribonucleases (89)

Protein domain: Barnase (49)

Bacillus amyloliquefaciens [TaxId: 1390] (49)

1a	d1b2xa_	A:
1b	d1b2xb_	B:
1c	d1b2xc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Nuclear Transport Factor 2; Chain: A, (517)

Homologous Superfamily: [code=3.10.450.30, no name defined] (159)

Bacillus amyloliquefaciens. Organism_taxid: 1390. (12)

1a	1b2xB00	B:3-110
1b	1b2xC00	C:3-110
1c	1b2xA00	A:2-110

(no "Pfam Domain" information available for 1B2X)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (RNBR_BACAM | P00648)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0004521	endoribonuclease activity	Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0004540	ribonuclease activity	Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
	GO:0090501	RNA phosphodiester bond hydrolysis	The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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