2QE9 - JenaLib

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Title :   CRYSTAL STRUCTURE OF A PUTATIVE METAL-DEPENDENT HYDROLASE (YIZA, BSU10800) FROM BACILLUS SUBTILIS AT 1.90 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   25 Jun 07 (Deposition) - 10 Jul 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A,B

Keywords :   Dinb/Yfit-Like Putative Metalloenzymes Fold, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Uncharacterized Protein Bsu10800 (Yp_054576. 1) From Bacillus Subtilis At 1. 90 A Resolution
To Be Published
PubMed: search

Molecule 1 - UNCHARACTERIZED PROTEIN YIZA
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	SPEEDET
	Expression System Strain	:	HK100
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YP_054576.1, YIZA, YUCC, BSU10800
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Strain	:	168

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 9)

No.	Name	Count	Type	Full Name
1	CIT	2	Ligand/Ion	CITRIC ACID
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
4	NI	2	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:44 , HIS A:124 , HIS A:128 , CIT A:201	BINDING SITE FOR RESIDUE NI A 200
2	AC2	SOFTWARE	HIS B:44 , HIS B:124 , HIS B:128 , CIT B:201	BINDING SITE FOR RESIDUE NI B 200
3	AC3	SOFTWARE	VAL A:35 , HIS A:44 , HIS A:124 , HIS A:128 , NI A:200 , HOH A:274 , HOH A:299 , HOH A:300	BINDING SITE FOR RESIDUE CIT A 201
4	AC4	SOFTWARE	EDO A:202 , VAL B:35 , HIS B:44 , HIS B:124 , HIS B:127 , HIS B:128 , NI B:200 , HOH B:290 , HOH B:312	BINDING SITE FOR RESIDUE CIT B 201
5	AC5	SOFTWARE	ALA A:146 , SER A:147 , PHE A:148 , HIS B:120 , HIS B:124 , CIT B:201	BINDING SITE FOR RESIDUE EDO A 202

(no "SS Bond" information available for 2QE9)

(no "Cis Peptide Bond" information available for 2QE9)

(no "SAP(SNP)/Variant" information available for 2QE9)

(no "PROSITE Motif" information available for 2QE9)

(no "Exon" information available for 2QE9)

Asymmetric/Biological 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:165
 aligned with YIZA_BACSU | Q7WY73 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:171
                                        1                                                                                                                                                              
                                     -  |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 
           YIZA_BACSU     - ------------MMKFFEYNWQVRDQWFTWCHQLTTEELLKNRLGGVENILYTLFHIIDVEYSWIRAIQGKEDIAVQFADYQTLNKVKSLSNTFRTEIIDVLQTHSDQIKDELVSVPWETGVLYTRDEILHHIIAHEIHHIGQLSVWARELKLSPVSASFIGRTLKPIHSY 159
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----2qe9A01 A:-6-159 dinb family like domain                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh......hhhhh.hhhhhhhhhhhhhhhhhhhhh..------..ee.......eehhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qe9 A -11 HHHHHENLYFQGmmKFFEYNWQVRDQWFTWCHQLTTEELLKNRLGGVENILYTLFHIIDVEYSWIRAIQGKEDIAVQFADYQTLNKVKSLSNTFRTEIIDVLQTH------ELVSVPWETGVLYTRDEILHHIIAHEIHHIGQLSVWARELKLSPVSASFIGRTLKPIHSY 159
                                    -2  ||     8        18        28        38        48        58        68        78        88    |    - |     108       118       128       138       148       158 
                                        1-MSE                                                                                      93    100                                                           
                                         2-MSE

Chain B from PDB  Type:PROTEIN  Length:162
 aligned with YIZA_BACSU | Q7WY73 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:162
                                       1                                                                                                                                                      
                                     - |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149  
           YIZA_BACSU     - -----------MMKFFEYNWQVRDQWFTWCHQLTTEELLKNRLGGVENILYTLFHIIDVEYSWIRAIQGKEDIAVQFADYQTLNKVKSLSNTFRTEIIDVLQTHSDQIKDELVSVPWETGVLYTRDEILHHIIAHEIHHIGQLSVWARELKLSPVSASFIGR 151
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ----2qe9B01 B:-6-151 dinb family like domain                                                                                                                       CATH domains
           Pfam domains (1) -----------DinB-2qe9B01 B:1-151                                                                                                                                    Pfam domains (1)
           Pfam domains (2) -----------DinB-2qe9B02 B:1-151                                                                                                                                    Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh......hhhhh.hhhhhhhhhhhhhhhhhhhhhhh.......eee.......eeehhhhhhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qe9 B -10 HHHHENLYFQGmmKFFEYNWQVRDQWFTWCHQLTTEELLKNRLGGVENILYTLFHIIDVEYSWIRAIQGKEDIAVQFADYQTLNKVKSLSNTFRTEIIDVLQTHSDQIKDELVSVPWETGVLYTRDEILHHIIAHEIHHIGQLSVWARELKLSPVSASFIGR 151
                                    -1 ||      9        19        29        39        49        59        69        79        89        99       109       119       129       139       149  
                                       1-MSE                                                                                                                                                  
                                        2-MSE

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 '\|'

(no "SCOP Domain" information available for 2QE9)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Four Helix Bundle (Hemerythrin (Met), subunit A) (300)

Homologous Superfamily: dinb family like domain (9)

Bacillus subtilis. Organism_taxid: 1423. Strain: 168. (1)

1a	2qe9A01	A:-6-159
1b	2qe9B01	B:-6-151

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DinB (11)

Family: DinB (1)

Bacillus subtilis (1)

1a	DinB-2qe9B01	B:1-151
1b	DinB-2qe9B02	B:1-151

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (YIZA_BACSU | Q7WY73)

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

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2qe9)

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	2qe9
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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CATH Domains (1, 2)

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