3LVZ - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   NEW REFINEMENT OF THE CRYSTAL STRUCTURE OF BJP-1, A SUBCLASS B3 METALLO-BETA-LACTAMASE OF BRADYRHIZOBIUM JAPONICUM

Authors :   J. D. Docquier, M. Benvenuti, V. Calderone, M. Stoczko, G. M. Rossolini S. Mangani

Date :   23 Feb 10 (Deposition) - 12 Jan 11 (Release) - 12 Jan 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Class B3 Metallo-Beta-Lactamase, Hydrolase, Beta-Lactam Hydrolysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. D. Docquier, M. Benvenuti, V. Calderone, M. Stoczko, N. Menciassi, G. M. Rossolini, S. Mangani
High-Resolution Crystal Structure Of The Subclass B3 Metallo-Beta-Lactamase Bjp-1: Rational Basis For Substrate Specificity And Interaction With Sulfonamides.
Antimicrob. Agents Chemother. V. 54 4343 2010
PubMed-ID: 20696874 | Reference-DOI: 10.1128/AAC.00409-10

Molecule 1 - BLR6230 PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-9A
	Expression System Strain	:	DH5
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BLR6230, BRADYRHIZOBIUM
	Organism Scientific	:	BRADYRHIZOBIUM JAPONICUM
	Organism Taxid	:	224911
	Strain	:	USDA 100
	Synonym	:	SUBCLASS B3 METALLO-BETA-LACTAMASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	ZN	6	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

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:101 , HIS A:103 , HIS A:177 , ZN A:296 , HOH A:302	BINDING SITE FOR RESIDUE ZN A 295
2	AC2	SOFTWARE	ASP A:105 , HIS A:106 , HIS A:242 , ZN A:295 , HOH A:299 , HOH A:302	BINDING SITE FOR RESIDUE ZN A 296
3	AC3	SOFTWARE	GLU A:158 , HIS A:172 , LYS A:229 , LYS A:294	BINDING SITE FOR RESIDUE ZN A 297
4	AC4	SOFTWARE	ASP B:105 , HIS B:106 , HIS B:242 , ZN B:296 , HOH B:298 , HOH B:482	BINDING SITE FOR RESIDUE ZN B 295
5	AC5	SOFTWARE	HIS B:101 , HIS B:103 , HIS B:177 , ZN B:295 , HOH B:482	BINDING SITE FOR RESIDUE ZN B 296
6	AC6	SOFTWARE	GLU B:158 , HIS B:172 , LYS B:229 , LYS B:294	BINDING SITE FOR RESIDUE ZN B 297

Asymmetric Unit

No.	Residues
1	A:181	-	A:201
2	B:181	-	B:201

(no "Cis Peptide Bond" information available for 3LVZ)

(no "SAP(SNP)/Variant" information available for 3LVZ)

(no "PROSITE Motif" information available for 3LVZ)

(no "Exon" information available for 3LVZ)

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:272
 aligned with Q89GW5_BRADU | Q89GW5 from UniProtKB/TrEMBL  Length:294

    Alignment length:272
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292  
         Q89GW5_BRADU    23 IKDFLAVAMKKWTAPFEPFQLIDNIYYVGTDGIAVYVIKTSQGLILMDTAMPQSTGMIKDNIAKLGFKVADIKLILNTHAHLDHTGGFAEIKKETGAQLVAGERDKPLLEGGYYPGDEKNEDLAFPAVKVDRAVKEGDRVTLGDTTLTAHATPGHSPGCTSWEMTVKDGKEDREVLFFCSGTVALNRLVGQPTYAGIVDDYRATFAKAKAMKIDVLLGPHPEVYGMQAKRAEMKDGAPNPFIKPGELVTYATSLSEDFDKQLAKQTAALEKK 294
               SCOP domains d3lvza_ A: automated matches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....eeee..eee........eeeee..eeeee...hhhhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhhh.eeeee..hhhhhhhh.......hhhhh.......eee....eeee..eeeeeee........eeeeeeeee..eeeeeee..................hhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lvz A  23 IKDFLAVAMKKWTAPFEPFQLIDNIYYVGTDGIAVYVIKTSQGLILMDTAMPQSTGMIKDNIAKLGFKVADIKLILNTHAHLDHTGGFAEIKKETGAQLVAGERDKPLLEGGYYPGDEKNEDLAFPAVKVDRAVKEGDRVTLGDTTLTAHATPGHSPGCTSWEMTVKDGKEDREVLFFCSGTVALNRLVGQPTYAGIVDDYRATFAKAKAMKIDVLLGPHPEVYGMQAKRAEMKDGAPNPFIKPGELVTYATSLSEDFDKQLAKQTAALEKK 294
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292

Chain B from PDB  Type:PROTEIN  Length:273
 aligned with Q89GW5_BRADU | Q89GW5 from UniProtKB/TrEMBL  Length:294

    Alignment length:273
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
         Q89GW5_BRADU    22 TIKDFLAVAMKKWTAPFEPFQLIDNIYYVGTDGIAVYVIKTSQGLILMDTAMPQSTGMIKDNIAKLGFKVADIKLILNTHAHLDHTGGFAEIKKETGAQLVAGERDKPLLEGGYYPGDEKNEDLAFPAVKVDRAVKEGDRVTLGDTTLTAHATPGHSPGCTSWEMTVKDGKEDREVLFFCSGTVALNRLVGQPTYAGIVDDYRATFAKAKAMKIDVLLGPHPEVYGMQAKRAEMKDGAPNPFIKPGELVTYATSLSEDFDKQLAKQTAALEKK 294
               SCOP domains d3lvzb_ B: automated matches                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh....eeee..eee........eeeee..eeeee...hhhhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhhh.eeeee..hhhhhhhh.......hhhhh.......eee....eeee..eeeeeee........eeeeeeeee..eeeeeee..................hhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lvz B  22 TIKDFLAVAMKKWTAPFEPFQLIDNIYYVGTDGIAVYVIKTSQGLILMDTAMPQSTGMIKDNIAKLGFKVADIKLILNTHAHLDHTGGFAEIKKETGAQLVAGERDKPLLEGGYYPGDEKNEDLAFPAVKVDRAVKEGDRVTLGDTTLTAHATPGHSPGCTSWEMTVKDGKEDREVLFFCSGTVALNRLVGQPTYAGIVDDYRATFAKAKAMKIDVLLGPHPEVYGMQAKRAEMKDGAPNPFIKPGELVTYATSLSEDFDKQLAKQTAALEKK 294
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291

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: Metallo-hydrolase/oxidoreductase (184)

Superfamily: Metallo-hydrolase/oxidoreductase (184)

Family: Zn metallo-beta-lactamase (93)

Protein domain: automated matches (30)

Bradyrhizobium japonicum [TaxId: 224911] (2)

1a	d3lvza_	A:
1b	d3lvzb_	B:

(no "CATH Domain" information available for 3LVZ)

(no "Pfam Domain" information available for 3LVZ)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q89GW5_BRADU | Q89GW5)

molecular function
	GO:0046872		metal ion binding		Interacting selectively and non-covalently with any metal ion.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3lvz)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
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	Q89GW5_BRADU \| Q89GW5	:	2gmn 3m8t

1k07	SUBCLASS B3 BETA-LACTAMASE FEZ-1 FROM FLUORIBACTER GORMANII
2gmn	SAME PROTEIN TO BE REPLACED BY THE PRESENT SUBMISSION
2h6a	B3 SUBCLASS BETA-LACTAMASE L1 FROM STENOTROPHOMONAS MALTOPHILIA

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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