1V3W - JenaLib

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Title :   STRUCTURE OF FERRIPYOCHELIN BINDING PROTEIN FROM PYROCOCCUS HORIKOSHII OT3

Authors :   J. Jeyakanthan, T. H. Tahirov, Riken Structural Genomics/Proteomi Initiative (Rsgi)

Date :   07 Nov 03 (Deposition) - 18 Nov 03 (Release) - 30 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Beta-Helix, Carbonic Anhydrase, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Jeyakanthan, S. Rangarajan, P. Mridula, S. P. Kanaujia, Y. Shiro, S. Kuramitsu, S. Yokoyama, K. Sekar
Observation Of A Calcium-Binding Site In The Gamma-Class Carbonic Anhydrase From Pyrococcus Horikoshii.
Acta Crystallogr. , Sect. D V. 64 1012 2008
PubMed-ID: 18931408 | Reference-DOI: 10.1107/S0907444908024323

Molecule 1 - FERRIPYOCHELIN BINDING PROTEIN
	Chains	:	A
	EC Number	:	4.2.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-11A
	Expression System Strain	:	BL21-CODON PLUS(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	70601
	Strain	:	OT3

		1
Asymmetric Unit	:	A
Biological Unit 1 (3x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 10)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	CL	1	Ligand/Ion	CHLORIDE ION
3	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
4	GOL	1	Ligand/Ion	GLYCEROL
5	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	9	Ligand/Ion	1,2-ETHANEDIOL
4	GOL	3	Ligand/Ion	GLYCEROL
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:65 , HIS A:82 , HIS A:87 , TYR A:159 , GOL A:1001 , HOH A:3007 , HOH A:3008	BINDING SITE FOR RESIDUE ZN A 3001
02	AC2	SOFTWARE	SER A:40 , ASN A:61	BINDING SITE FOR RESIDUE CA A 3002
03	AC3	SOFTWARE	HOH A:3009 , HOH A:3010 , HOH A:3011 , HOH A:3012 , HOH A:3013 , HOH A:3016	BINDING SITE FOR RESIDUE CA A 3003
04	AC4	SOFTWARE	GLU A:164 , HOH A:3014 , HOH A:3015	BINDING SITE FOR RESIDUE CA A 3004
05	AC5	SOFTWARE	ASN A:83	BINDING SITE FOR RESIDUE CA A 3005
06	AC6	SOFTWARE	LYS A:125 , VAL A:140 , HOH A:3195	BINDING SITE FOR RESIDUE CL A 3006
07	AC7	SOFTWARE	ASN A:22 , VAL A:24 , SER A:40 , HOH A:3187	BINDING SITE FOR RESIDUE EDO A 2001
08	AC8	SOFTWARE	GLU A:21 , ASN A:22 , HOH A:3188	BINDING SITE FOR RESIDUE EDO A 2002
09	AC9	SOFTWARE	SER A:100 , GLY A:118	BINDING SITE FOR RESIDUE EDO A 2003
10	BC1	SOFTWARE	GLN A:59 , GLY A:81 , HIS A:82 , HIS A:87 , ASN A:155 , TYR A:159 , ZN A:3001 , HOH A:3007 , HOH A:3062 , HOH A:3118 , HOH A:3158	BINDING SITE FOR RESIDUE GOL A 1001

(no "SS Bond" information available for 1V3W)

Asymmetric Unit

No.	Residues
1	Val A:136	-	Pro A:137

(no "SAP(SNP)/Variant" information available for 1V3W)

(no "PROSITE Motif" information available for 1V3W)

(no "Exon" information available for 1V3W)

Asymmetric Unit

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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:173
 aligned with O59257_PYRHO | O59257 from UniProtKB/TrEMBL  Length:173

    Alignment length:173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   
         O59257_PYRHO     1 MAIYEINGKKPRIHPSAFVDENAVVIGDVVLEEKTSVWPSAVLRGDIEQIYVGKYSNVQDNVSIHTSHGYPTEIGEYVTIGHNAMVHGAKVGNYVIIGISSVILDGAKIGDHVIIGAGAVVPPNKEIPDYSLVLGVPGKVVRQLTEEEIEWTKKNAEIYVELAEKHIKGRKRI 173
               SCOP domains d1v3wa_ A: Ferripyochelin binding protein                                                                                                                                     SCOP domains
               CATH domains 1v3wA00 A:1-173 Hexapeptide repeat proteins                                                                                                                                   CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------Hexapep-1v3wA01 A:88-123            -------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------Hexapep-1v3wA02 A:88-123            -------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------Hexapep-1v3wA03 A:88-123            -------------------------------------------------- Pfam domains (3)
         Sec.struct. author .eee.......ee....ee....eeeeeeee....ee....eeeeeeeeeee....ee....eee......eee....ee....eee..ee...eee....ee....ee...eee....ee....ee...eeee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v3w A   1 MAIYEINGKKPRIHPSAFVDENAVVIGDVVLEEKTSVWPSAVLRGDIEQIYVGKYSNVQDNVSIHTSHGYPTEIGEYVTIGHNAMVHGAKVGNYVIIGISSVILDGAKIGDHVIIGAGAVVPPNKEIPDYSLVLGVPGKVVRQLTEEEIEWTKKNAEIYVELAEKHIKGRKRI 173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

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: All beta proteins (24004)

Fold: Single-stranded left-handed beta-helix (154)

Superfamily: Trimeric LpxA-like enzymes (147)

Family: gamma-carbonic anhydrase-like (17)

Protein domain: Ferripyochelin binding protein (3)

Pyrococcus horikoshii [TaxId: 53953] (3)

d1v3wa_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: 3 Solenoid (196)

Topology: UDP N-Acetylglucosamine Acyltransferase; domain 1 (90)

Homologous Superfamily: Hexapeptide repeat proteins (85)

Pyrococcus horikoshii ot3. Organism_taxid: 70601. Strain: ot3. (3)

1v3wA00

A:1-173

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Hexapep] (52)

Family: Hexapep (52)

Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (2)

1a	Hexapep-1v3wA01	A:88-123
1b	Hexapep-1v3wA02	A:88-123
1c	Hexapep-1v3wA03	A:88-123

Asymmetric Unit(hide GO term definitions)

Chain A (O59257_PYRHO | O59257)

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
		Val A:136 - Pro A:137	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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