2RD9 - JenaLib

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Title :   CRYSTAL STRUCTURE OF A PUTATIVE YFIT-LIKE METAL-DEPENDENT HYDROLASE (BH0186) FROM BACILLUS HALODURANS C-125 AT 2.30 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   21 Sep 07 (Deposition) - 09 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   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 Yfit-Like Putative Metal-Dependent Hydrolase (Np_241052. 1) From Bacillus Halodurans At 2. 30 A Resolution
To Be Published
PubMed: search

Molecule 1 - BH0186 PROTEIN
	Atcc	:	BAA-125
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	SPEEDET
	Expression System Strain	:	HK100
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NP_241052.1, BH0186
	Organism Scientific	:	BACILLUS HALODURANS C-125
	Organism Taxid	:	272558
	Strain	:	C-125, DSM 18197, FERM 7344, JCM 9153

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 28)

No.	Name	Count	Type	Full Name
1	GOL	7	Ligand/Ion	GLYCEROL
2	IMD	5	Ligand/Ion	IMIDAZOLE
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
4	NI	4	Ligand/Ion	NICKEL (II) ION

Biological Unit 1 (3, 13)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	IMD	3	Ligand/Ion	IMIDAZOLE
3	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
4	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 2 (3, 11)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	IMD	2	Ligand/Ion	IMIDAZOLE
3	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
4	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 3 (3, 24)

No.	Name	Count	Type	Full Name
1	GOL	7	Ligand/Ion	GLYCEROL
2	IMD	5	Ligand/Ion	IMIDAZOLE
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
4	NI	-1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:48 , HIS A:142 , HIS A:146 , IMD A:301 , HOH A:421 , HIS D:-9	BINDING SITE FOR RESIDUE NI A 300
02	AC2	SOFTWARE	HIS B:-9 , HIS C:48 , HIS C:142 , HIS C:146 , IMD C:302 , HOH C:384	BINDING SITE FOR RESIDUE NI C 300
03	AC3	SOFTWARE	IMD A:303 , HOH A:393 , HIS B:48 , HIS B:142 , HIS B:146 , HIS C:-9	BINDING SITE FOR RESIDUE NI B 300
04	AC4	SOFTWARE	HIS A:-9 , IMD C:301 , HOH C:382 , HIS D:48 , HIS D:142 , HIS D:146	BINDING SITE FOR RESIDUE NI D 300
05	AC5	SOFTWARE	HIS A:142 , HIS A:146 , NI A:300 , HOH A:421 , TYR B:168 , LEU B:169 , ILE B:171 , HIS D:-9	BINDING SITE FOR RESIDUE IMD A 301
06	AC6	SOFTWARE	HIS A:-9 , TYR C:168 , LEU C:169 , ILE C:171 , HOH C:382 , HIS D:142 , HIS D:146 , NI D:300	BINDING SITE FOR RESIDUE IMD C 301
07	AC7	SOFTWARE	HIS B:-9 , HIS C:142 , HIS C:146 , NI C:300 , TYR D:168 , LEU D:169 , ILE D:171	BINDING SITE FOR RESIDUE IMD C 302
08	AC8	SOFTWARE	MSE A:5 , GLN A:113 , SER A:114 , ARG B:78	BINDING SITE FOR RESIDUE IMD A 302
09	AC9	SOFTWARE	TYR A:168 , LEU A:169 , ILE A:171 , HOH A:393 , HOH A:394 , HIS B:142 , HIS B:146 , NI B:300 , HIS C:-9	BINDING SITE FOR RESIDUE IMD A 303
10	BC1	SOFTWARE	TRP A:40 , GLU A:44 , HOH A:355	BINDING SITE FOR RESIDUE GOL A 304
11	BC2	SOFTWARE	GLN A:-1 , TYR A:-3 , LEU A:-4 , GLY B:36 , TYR B:37 , LYS B:156 , GLU C:167	BINDING SITE FOR RESIDUE GOL A 305
12	BC3	SOFTWARE	PHE A:79 , SER A:80 , HOH A:362 , MSE D:5 , ARG D:109 , HOH D:348 , HOH D:428 , HOH D:436	BINDING SITE FOR RESIDUE GOL D 301
13	BC4	SOFTWARE	ALA B:116 , GLU B:119 , ARG B:120 , PHE C:63 , GLN C:66 , GLU C:67 , HOH C:380	BINDING SITE FOR RESIDUE GOL B 301
14	BC5	SOFTWARE	HIS A:-12 , HOH A:405 , TRP D:40 , GLU D:44 , GLU D:51 , HOH D:396	BINDING SITE FOR RESIDUE GOL D 302
15	BC6	SOFTWARE	TYR C:43 , ASN C:86 , ALA C:87 , VAL C:88 , PRO C:89 , ILE C:90 , HOH C:360 , HOH C:417	BINDING SITE FOR RESIDUE GOL C 303

(no "SS Bond" information available for 2RD9)

Asymmetric Unit

No.	Residues
1	Asn D:86	-	Ala D:87

(no "SAP(SNP)/Variant" information available for 2RD9)

(no "PROSITE Motif" information available for 2RD9)

(no "Exon" information available for 2RD9)

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:189
 aligned with Q9KGB8_BACHD | Q9KGB8 from UniProtKB/TrEMBL  Length:174

    Alignment length:189
                                           1                                                                                                                                                                             
                                     -     |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165         
         Q9KGB8_BACHD     - ---------------MNFQMNEAIQLLERTPKTLEVFLEGLSDSWHQCNEGYETWTVYEVVVHLIEAEKTNWIPRLRFILQEGEHKPFPAFDRFSHLNQSNAVPISERFKEFQQLRKENLNTLRSLVQSEADLERTGAHPAFGVVKVRELLSAWVVHDLTHIAQIVRSMAKRYDTDVGPWKEYLGILND 174
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----2rd9A01 A:-9-171 dinb family like domain                                                                                                                                             --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhh......hhhhhhhhhhhhhhhhhhhhh..hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.ee......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeee...eeeehhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rd9 A -14 KIHHHHHHENLYFQGmNFQmNEAIQLLERTPKTLEVFLEGLSDSWHQCNEGYETWTVYEVVVHLIEAEKTNWIPRLRFILQEGEHKPFPAFDRFSHLNQSNAVPISERFKEFQQLRKENLNTLRSLVQSEADLERTGAHPAFGVVKVRELLSAWVVHDLTHIAQIVRSmAKRYDTDVGPWKEYLGILND 174
                                    -5     |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165         
                                           1-MSE                                                                                                                                                  154-MSE                
                                               5-MSE

Chain B from PDB  Type:PROTEIN  Length:184
 aligned with Q9KGB8_BACHD | Q9KGB8 from UniProtKB/TrEMBL  Length:174

    Alignment length:190
                                            1                                                                                                                                                                             
                                     -      |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174
         Q9KGB8_BACHD     - ----------------MNFQMNEAIQLLERTPKTLEVFLEGLSDSWHQCNEGYETWTVYEVVVHLIEAEKTNWIPRLRFILQEGEHKPFPAFDRFSHLNQSNAVPISERFKEFQQLRKENLNTLRSLVQSEADLERTGAHPAFGVVKVRELLSAWVVHDLTHIAQIVRSMAKRYDTDVGPWKEYLGILND 174
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------2rd9B01 B:-9-171 dinb family like domain                                                                                                                                             --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....hhhhh......hhhhhhhhhhhhhhhhhhhhh..hhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......------....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeee...eeeehhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rd9 B -15 DKIHHHHHHENLYFQGmNFQmNEAIQLLERTPKTLEVFLEGLSDSWHQCNEGYETWTVYEVVVHLIEAEKTNWIPRLRFILQEGEHKPFPAFDR------SNAVPISERFKEFQQLRKENLNTLRSLVQSEADLERTGAHPAFGVVKVRELLSAWVVHDLTHIAQIVRSmAKRYDTDVGPWKEYLGILND 174
                                    -6      |  4|       14        24        34        44        54        64        74   |     -|       94       104       114       124       134       144       154       164       174
                                            1-MSE                                                                       78     85                                                                  154-MSE                
                                                5-MSE

Chain C from PDB  Type:PROTEIN  Length:186
 aligned with Q9KGB8_BACHD | Q9KGB8 from UniProtKB/TrEMBL  Length:174

    Alignment length:186
                                        1                                                                                                                                                                             
                                     -  |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168      
         Q9KGB8_BACHD     - ------------MNFQMNEAIQLLERTPKTLEVFLEGLSDSWHQCNEGYETWTVYEVVVHLIEAEKTNWIPRLRFILQEGEHKPFPAFDRFSHLNQSNAVPISERFKEFQQLRKENLNTLRSLVQSEADLERTGAHPAFGVVKVRELLSAWVVHDLTHIAQIVRSMAKRYDTDVGPWKEYLGILND 174
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains --2rd9C01 C:-9-171 dinb family like domain                                                                                                                                             --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhh......hhhhhhhhhhhhhhhhhhhhh..hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........ee......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeee...eeeehhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2rd9 C -11 HHHHHENLYFQGmNFQmNEAIQLLERTPKTLEVFLEGLSDSWHQCNEGYETWTVYEVVVHLIEAEKTNWIPRLRFILQEGEHKPFPAFDRFSHLNQSNAVPISERFKEFQQLRKENLNTLRSLVQSEADLERTGAHPAFGVVKVRELLSAWVVHDLTHIAQIVRSmAKRYDTDVGPWKEYLGILND 174
                                    -2  |   |  8        18        28        38        48        58        68        78        88        98       108       118       128       138       148     | 158       168      
                                        1-MSE                                                                                                                                                  154-MSE                
                                            5-MSE

Chain D from PDB  Type:PROTEIN  Length:189
 aligned with Q9KGB8_BACHD | Q9KGB8 from UniProtKB/TrEMBL  Length:174

    Alignment length:189
                                           1                                                                                                                                                                             
                                     -     |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165         
         Q9KGB8_BACHD     - ---------------MNFQMNEAIQLLERTPKTLEVFLEGLSDSWHQCNEGYETWTVYEVVVHLIEAEKTNWIPRLRFILQEGEHKPFPAFDRFSHLNQSNAVPISERFKEFQQLRKENLNTLRSLVQSEADLERTGAHPAFGVVKVRELLSAWVVHDLTHIAQIVRSMAKRYDTDVGPWKEYLGILND 174
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----2rd9D01 D:-9-171 dinb family like domain                                                                                                                                             --- CATH domains
           Pfam domains (1) -------------------------DinB_2-2rd9D01 D:11-150                                                                                                                     ------------------------ Pfam domains (1)
           Pfam domains (2) -------------------------DinB_2-2rd9D02 D:11-150                                                                                                                     ------------------------ Pfam domains (2)
           Pfam domains (3) -------------------------DinB_2-2rd9D03 D:11-150                                                                                                                     ------------------------ Pfam domains (3)
           Pfam domains (4) -------------------------DinB_2-2rd9D04 D:11-150                                                                                                                     ------------------------ Pfam domains (4)
         Sec.struct. author .ee....hhhhh......hhhhhhhhhhhhhhhhhhhhh..hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeee...eeeehhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rd9 D -14 KIHHHHHHENLYFQGmNFQmNEAIQLLERTPKTLEVFLEGLSDSWHQCNEGYETWTVYEVVVHLIEAEKTNWIPRLRFILQEGEHKPFPAFDRFSHLNQSNAVPISERFKEFQQLRKENLNTLRSLVQSEADLERTGAHPAFGVVKVRELLSAWVVHDLTHIAQIVRSmAKRYDTDVGPWKEYLGILND 174
                                    -5     |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165         
                                           1-MSE                                                                                                                                                  154-MSE                
                                               5-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 2RD9)

Asymmetric 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 halodurans c-125. Organism_taxid: 272558. Strain: c-125, dsm18197, ferm 7344, jcm 9153. (1)

1a	2rd9B01	B:-9-171
1b	2rd9A01	A:-9-171
1c	2rd9C01	C:-9-171
1d	2rd9D01	D:-9-171

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DinB (11)

Family: DinB_2 (5)

Bacillus halodurans (1)

1a	DinB_2-2rd9D01	D:11-150
1b	DinB_2-2rd9D02	D:11-150
1c	DinB_2-2rd9D03	D:11-150
1d	DinB_2-2rd9D04	D:11-150

Asymmetric Unit(hide GO term definitions)

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		Asn D:86 - Ala D:87	[ RasMol ]

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