1J31 - JenaLib

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Title :   CRYSTAL STRUCTURE OF HYPOTHETICAL PROTEIN PH0642 FROM PYROCOCCUS HORIKOSHII

Authors :   N. Sakai, Y. Tajika, M. Yao, N. Watanabe, I. Tanaka

Date :   16 Jan 03 (Deposition) - 09 Mar 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Alpha-Beta-Beta-Alpha Sandwich, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Sakai, Y. Tajika, M. Yao, N. Watanabe, I. Tanaka
Crystal Structure Of Hypothetical Protein Ph0642 From Pyrococcus Horikoshii At 1. 6A Resolution.
Proteins V. 57 869 2004
PubMed-ID: 15390259 | Reference-DOI: 10.1002/PROT.20259

Molecule 1 - HYPOTHETICAL PROTEIN PH0642
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-22B(+)
	Expression System Strain	:	BL21-CODONPLUS(DE3)-RIL-X
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PH0642
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	70601
	Strain	:	OT3

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 32)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	MSE	28	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 16)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	MSE	14	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 16)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	MSE	14	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:149 , LEU A:172 , VAL A:173 , MSE A:174 , HOH A:1345	BINDING SITE FOR RESIDUE ACT A 1301
2	AC2	SOFTWARE	TRP B:149 , LEU B:172 , VAL B:173 , MSE B:174 , HOH B:2314	BINDING SITE FOR RESIDUE ACT B 2301
3	AC3	SOFTWARE	TRP C:149 , LEU C:172 , VAL C:173 , MSE C:174 , HOH C:3313	BINDING SITE FOR RESIDUE ACT C 3301
4	AC4	SOFTWARE	TRP D:149 , LEU D:172 , VAL D:173 , MSE D:174 , HOH D:4309	BINDING SITE FOR RESIDUE ACT D 4301

(no "SS Bond" information available for 1J31)

Asymmetric Unit

No.	Residues
1	Ile A:63	-	Pro A:64
2	Ile B:63	-	Pro B:64
3	Ile C:63	-	Pro C:64
4	Ile D:63	-	Pro D:64

(no "SAP(SNP)/Variant" information available for 1J31)

(no "PROSITE Motif" information available for 1J31)

(no "Exon" information available for 1J31)

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:262
 aligned with O58376_PYRHO | O58376 from UniProtKB/TrEMBL  Length:262

    Alignment length:262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260  
         O58376_PYRHO     1 MVKVGYIQMEPKILELDKNYSKAEKLIKEASKEGAKLVVLPELFDTGYNFESREEVFDVAQQIPEGETTTFLMELARELGLYIVAGTAEKSGNYLYNSAVVVGPRGYIGKYRKIHLFYREKVFFEPGDLGFKVFDIGFAKVGVMICFDWFFPESARTLALKGAEIIAHPANLVMPYAPRAMPIRALENRVYTITADRVGEERGLKFIGKSLIASPKAEVLSIASETEEEIGVVEIDLNLARNKRLNDMNDIFKDRREEYYFR 262
               SCOP domains d1j31a_ A: Hypothetical protein PH0642                                                                                                                                                                                                                                 SCOP domains
               CATH domains -1j31A00 A:2-262  [code=3.60.110.10, no name defined]                                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhhhhhhhh...eee............hhhhhhh.......hhhhhhhhhhhhhhh.eeeeeeeeee..eeeeeeeeee..eeeeeee......hhhhhh........eee....eeee.hhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhh.eeeee....ee..ee.....eee.....eeee......eeeeeeehhhhhhh.eee..ee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j31 A   1 mVKVGYIQmEPKILELDKNYSKAEKLIKEASKEGAKLVVLPELFDTGYNFESREEVFDVAQQIPEGETTTFLmELARELGLYIVAGTAEKSGNYLYNSAVVVGPRGYIGKYRKIHLFYREKVFFEPGDLGFKVFDIGFAKVGVmICFDWFFPESARTLALKGAEIIAHPANLVmPYAPRAmPIRALENRVYTITADRVGEERGLKFIGKSLIASPKAEVLSIASETEEEIGVVEIDLNLARNKRLNDmNDIFKDRREEYYFR 262
                            |       10        20        30        40        50        60        70  |     80        90       100       110       120       130       140   |   150       160       170   |   180|      190       200       210       220       230       240       250       260  
                            |       9-MSE                                                          73-MSE                                                                144-MSE                       174-MSE  |                                                                248-MSE          
                            1-MSE                                                                                                                                                                             181-MSE

Chain B from PDB  Type:PROTEIN  Length:262
 aligned with O58376_PYRHO | O58376 from UniProtKB/TrEMBL  Length:262

    Alignment length:262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260  
         O58376_PYRHO     1 MVKVGYIQMEPKILELDKNYSKAEKLIKEASKEGAKLVVLPELFDTGYNFESREEVFDVAQQIPEGETTTFLMELARELGLYIVAGTAEKSGNYLYNSAVVVGPRGYIGKYRKIHLFYREKVFFEPGDLGFKVFDIGFAKVGVMICFDWFFPESARTLALKGAEIIAHPANLVMPYAPRAMPIRALENRVYTITADRVGEERGLKFIGKSLIASPKAEVLSIASETEEEIGVVEIDLNLARNKRLNDMNDIFKDRREEYYFR 262
               SCOP domains d1j31b_ B: Hypothetical protein PH0642                                                                                                                                                                                                                                 SCOP domains
               CATH domains -1j31B00 B:2-262  [code=3.60.110.10, no name defined]                                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhhhhhhhh...eee............hhhhhhh..ee...hhhhhhhhhhhhhhh.eeeeeeeeee..eeeeeeeeee..eeeeeee......hhhhhh........eee....eeee.hhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhh.eeeeee...ee..ee.....eee.....eeee......eeeeeee.hhhhhh.eee..ee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j31 B   1 mVKVGYIQmEPKILELDKNYSKAEKLIKEASKEGAKLVVLPELFDTGYNFESREEVFDVAQQIPEGETTTFLmELARELGLYIVAGTAEKSGNYLYNSAVVVGPRGYIGKYRKIHLFYREKVFFEPGDLGFKVFDIGFAKVGVmICFDWFFPESARTLALKGAEIIAHPANLVmPYAPRAmPIRALENRVYTITADRVGEERGLKFIGKSLIASPKAEVLSIASETEEEIGVVEIDLNLARNKRLNDmNDIFKDRREEYYFR 262
                            |       10        20        30        40        50        60        70  |     80        90       100       110       120       130       140   |   150       160       170   |   180|      190       200       210       220       230       240       250       260  
                            1-MSE   9-MSE                                                          73-MSE                                                                144-MSE                       174-MSE  |                                                                248-MSE          
                                                                                                                                                                                                              181-MSE

Chain C from PDB  Type:PROTEIN  Length:262
 aligned with O58376_PYRHO | O58376 from UniProtKB/TrEMBL  Length:262

    Alignment length:262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260  
         O58376_PYRHO     1 MVKVGYIQMEPKILELDKNYSKAEKLIKEASKEGAKLVVLPELFDTGYNFESREEVFDVAQQIPEGETTTFLMELARELGLYIVAGTAEKSGNYLYNSAVVVGPRGYIGKYRKIHLFYREKVFFEPGDLGFKVFDIGFAKVGVMICFDWFFPESARTLALKGAEIIAHPANLVMPYAPRAMPIRALENRVYTITADRVGEERGLKFIGKSLIASPKAEVLSIASETEEEIGVVEIDLNLARNKRLNDMNDIFKDRREEYYFR 262
               SCOP domains d1j31c_ C: Hypothetical protein PH0642                                                                                                                                                                                                                                 SCOP domains
               CATH domains -1j31C00 C:2-262  [code=3.60.110.10, no name defined]                                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhhhhhhhh...eee............hhhhhhhhh.....hhhhhhhhhhhhhhh.eeeeeeeeee..eeeeeeeeee..eeeeeee......hhhhhh........eee....eeee.hhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhh.eeeee....ee..ee.....eee.....eeee......eeeeeeehhhhhhh.eee..ee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j31 C   1 mVKVGYIQmEPKILELDKNYSKAEKLIKEASKEGAKLVVLPELFDTGYNFESREEVFDVAQQIPEGETTTFLmELARELGLYIVAGTAEKSGNYLYNSAVVVGPRGYIGKYRKIHLFYREKVFFEPGDLGFKVFDIGFAKVGVmICFDWFFPESARTLALKGAEIIAHPANLVmPYAPRAmPIRALENRVYTITADRVGEERGLKFIGKSLIASPKAEVLSIASETEEEIGVVEIDLNLARNKRLNDmNDIFKDRREEYYFR 262
                            |       10        20        30        40        50        60        70  |     80        90       100       110       120       130       140   |   150       160       170   |   180|      190       200       210       220       230       240       250       260  
                            1-MSE   9-MSE                                                          73-MSE                                                                144-MSE                       174-MSE  |                                                                248-MSE          
                                                                                                                                                                                                              181-MSE

Chain D from PDB  Type:PROTEIN  Length:262
 aligned with O58376_PYRHO | O58376 from UniProtKB/TrEMBL  Length:262

    Alignment length:262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260  
         O58376_PYRHO     1 MVKVGYIQMEPKILELDKNYSKAEKLIKEASKEGAKLVVLPELFDTGYNFESREEVFDVAQQIPEGETTTFLMELARELGLYIVAGTAEKSGNYLYNSAVVVGPRGYIGKYRKIHLFYREKVFFEPGDLGFKVFDIGFAKVGVMICFDWFFPESARTLALKGAEIIAHPANLVMPYAPRAMPIRALENRVYTITADRVGEERGLKFIGKSLIASPKAEVLSIASETEEEIGVVEIDLNLARNKRLNDMNDIFKDRREEYYFR 262
               SCOP domains d1j31d_ D: Hypothetical protein PH0642                                                                                                                                                                                                                                 SCOP domains
               CATH domains -1j31D00 D:2-262  [code=3.60.110.10, no name defined]                                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhhhhhhhh...eee............hhhhhhh.......hhhhhhhhhhhhhhh.eeeeeeeeee..eeeeeeeeee..eeeeeee......hhhhhh........eee....eeee.hhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhh.eeeee....ee..ee.....eee.....eeee......eeeeeee.hhhhhh.eee..ee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j31 D   1 mVKVGYIQmEPKILELDKNYSKAEKLIKEASKEGAKLVVLPELFDTGYNFESREEVFDVAQQIPEGETTTFLmELARELGLYIVAGTAEKSGNYLYNSAVVVGPRGYIGKYRKIHLFYREKVFFEPGDLGFKVFDIGFAKVGVmICFDWFFPESARTLALKGAEIIAHPANLVmPYAPRAmPIRALENRVYTITADRVGEERGLKFIGKSLIASPKAEVLSIASETEEEIGVVEIDLNLARNKRLNDmNDIFKDRREEYYFR 262
                            |       10        20        30        40        50        60        70  |     80        90       100       110       120       130       140   |   150       160       170   |   180|      190       200       210       220       230       240       250       260  
                            1-MSE   9-MSE                                                          73-MSE                                                                144-MSE                       174-MSE  |                                                                248-MSE          
                                                                                                                                                                                                              181-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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Carbon-nitrogen hydrolase (18)

Superfamily: Carbon-nitrogen hydrolase (18)

Family: Carbamilase (13)

Protein domain: Hypothetical protein PH0642 (1)

Pyrococcus horikoshii [TaxId: 53953] (1)

1a	d1j31a_	A:
1b	d1j31b_	B:
1c	d1j31c_	C:
1d	d1j31d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 4-Layer Sandwich (459)

Topology: Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase (14)

Homologous Superfamily: [code=3.60.110.10, no name defined] (14)

Pyrococcus horikoshii ot3. Organism_taxid: 70601. Strain: ot3. (1)

1a	1j31A00	A:2-262
1b	1j31B00	B:2-262
1c	1j31C00	C:2-262
1d	1j31D00	D:2-262

(no "Pfam Domain" information available for 1J31)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (O58376_PYRHO | O58376)

molecular function
	GO:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
biological process
	GO:0006807	nitrogen compound metabolic process	The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.

Asymmetric Unit
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		Ile B:63 - Pro B:64	[ RasMol ]
		Ile C:63 - Pro C:64	[ RasMol ]
		Ile D:63 - Pro D:64	[ RasMol ]

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