4ARV - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   YERSINIA KRISTENSENII PHYTASE APO FORM

Authors :   A. Ariza, O. V. Moroz, E. B. Blagova, J. P. Turkenburg, J. Vevodova, S. Ro J. Vind, C. Sjoholm, S. F. Lassen, L. De Maria, V. Glitsoe, L. K. Skov, K. S. Wilson

Date :   26 Apr 12 (Deposition) - 08 May 13 (Release) - 05 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.67

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

Keywords :   Hydrolase, 6-Phytase, Myo-Inositol Hexakis Phosphate Phosphohydrolase, Histidine Acid Phosphatase, Happ (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Ariza, O. V. Moroz, E. V. Blagova, J. P. Turkenburg, J. Waterman, S. M. Roberts, J. Vind, C. Sjoholm, S. F. Lassen, L. De Maria, V. Glitsoe, L. K. Skov, K. S. Wilson
Degradation Of Phytate By The 6-Phytase From Hafnia Alvei: A Combined Structural And Solution Study.
Plos One V. 8 65062 2013
PubMed-ID: 23741456 | Reference-DOI: 10.1371/JOURNAL.PONE.0065062

Molecule 1 - PHYTASE
	Chains	:	A, B
	EC Number	:	3.1.3.26
	Engineered	:	YES
	Expression System	:	ASPERGILLUS ORYZAE
	Expression System Taxid	:	5062
	Organism Scientific	:	YERSINIA KRISTENSENII
	Organism Taxid	:	28152

		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 (4, 12)

No.	Name	Count	Type	Full Name
1	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
2	P15	1	Ligand/Ion	2,5,8,11,14,17-HEXAOXANONADECAN-19-OL
3	PO4	4	Ligand/Ion	PHOSPHATE ION
4	TOE	1	Ligand/Ion	2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	P15	-1	Ligand/Ion	2,5,8,11,14,17-HEXAOXANONADECAN-19-OL
3	PO4	2	Ligand/Ion	PHOSPHATE ION
4	TOE	1	Ligand/Ion	2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	P15	1	Ligand/Ion	2,5,8,11,14,17-HEXAOXANONADECAN-19-OL
3	PO4	2	Ligand/Ion	PHOSPHATE ION
4	TOE	-1	Ligand/Ion	2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:17 , HIS A:18 , ARG A:21 , ARG A:92 , HIS A:306 , ASP A:307 , HOH A:2561	BINDING SITE FOR RESIDUE PO4 A1415
02	AC2	SOFTWARE	ASP A:90 , ARG A:92 , HIS A:126 , HIS A:306 , HOH A:2164 , HOH A:2170 , HOH A:2226 , HOH A:2227 , HOH A:2561 , HOH A:2562	BINDING SITE FOR RESIDUE PO4 A1416
03	AC3	SOFTWARE	ARG A:21 , PRO A:23 , THR A:24 , THR A:218 , GLU A:221 , ILE A:222 , HOH A:2037 , HOH A:2414	BINDING SITE FOR RESIDUE EDO A1417
04	AC4	SOFTWARE	GLN A:183 , HOH A:2563	BINDING SITE FOR RESIDUE EDO A1418
05	AC5	SOFTWARE	LYS A:134 , HIS A:268 , SER A:411 , HOH A:2428 , HOH A:2564	BINDING SITE FOR RESIDUE EDO A1419
06	AC6	SOFTWARE	TYR A:7 , TYR A:70 , ASN A:392 , HOH A:2002 , HOH A:2566	BINDING SITE FOR RESIDUE TOE A1420
07	AC7	SOFTWARE	ARG B:17 , HIS B:18 , ARG B:21 , ARG B:92 , HIS B:306 , ASP B:307 , HOH B:2187	BINDING SITE FOR RESIDUE PO4 B1415
08	AC8	SOFTWARE	ASP B:90 , ARG B:92 , HIS B:126 , HIS B:306 , HOH B:2182 , HOH B:2187 , HOH B:2188 , HOH B:2262 , HOH B:2263	BINDING SITE FOR RESIDUE PO4 B1416
09	AC9	SOFTWARE	ARG B:21 , PRO B:23 , THR B:24 , THR B:218 , GLU B:221 , ILE B:222 , HOH B:2039 , HOH B:2438	BINDING SITE FOR RESIDUE EDO B1417
10	BC1	SOFTWARE	GLY B:167 , ASN B:171 , PHE B:172 , SER B:173 , HOH B:2345	BINDING SITE FOR RESIDUE EDO B1418
11	BC2	SOFTWARE	VAL B:207 , MET B:259 , ALA B:260 , LYS B:269 , THR B:308 , ASN B:312 , HOH B:2388 , HOH B:2591	BINDING SITE FOR RESIDUE EDO B1419
12	BC3	SOFTWARE	TYR B:7 , TYR B:70 , TRP B:341 , ILE B:378 , ASN B:392 , HOH B:2002 , HOH B:2592 , HOH B:2593 , HOH B:2594	BINDING SITE FOR RESIDUE P15 B1420

Asymmetric Unit

No.	Residues
1	A:77	-	A:108
2	A:133	-	A:412
3	A:178	-	A:188
4	A:386	-	A:395
5	B:77	-	B:108
6	B:133	-	B:412
7	B:178	-	B:188
8	B:386	-	B:395

(no "Cis Peptide Bond" information available for 4ARV)

(no "SAP(SNP)/Variant" information available for 4ARV)

(no "PROSITE Motif" information available for 4ARV)

(no "Exon" information available for 4ARV)

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:409
 aligned with H9TUK6_YERKR | H9TUK6 from UniProtKB/TrEMBL  Length:441

    Alignment length:409
                                    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       302       312       322       332       342       352       362       372       382       392       402       412       422       432         
         H9TUK6_YERKR    33 GYTLERVVILSRHGVRSPTKQTQLMNDVTPDKWPQWPVKAGYLTPRGAGLVTLMGGFYGDYFRSYGLLPAGCPADESIYVQADVDQRTRLTGQAFLDGIAPDCGLKVHYQADLKKIDPLFHTVEAGVCKLDPEKTHQAVEKRLGGPLNELSQRYAKPFALMGEVLNFSASPYCNSLQQKGKACDFATFAANEIEVNKEGTKVSLSGPLALSSTLGEIFLLQNSQAMPDVAWNRLSGEENWISLLSLHNAQFDLMAKTPYIARHKGTPLLQQIDTALVLQRDAQGQTLPLSPQTKLLFLGGHDTNIANIAGMLGANWQLPQQPDNTPPGGGLVFELWQNPDNHQRYVAVKMFYQTMEQLRNADKLDLKNNPARIVPIAIEGCENEGDNKLCQLETFQKKVAQVIEPSCHI 441
               SCOP domains d4arva_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.........hhhhhhh...............hhhhhhhhhhhhhhhhhhhhhh............eeeee..hhhhhhhhhhhhhhhh.......ee.....................hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh...eeee......eeeehhhhhhhhhhhhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................eeeeeehhhhhhhhhhhhh................eeeeeeee......eeeeeeeee.hhhhhhh...........eeee..............eehhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4arv A   6 GYTLERVVILSRHGVRSPTKQTQLMNDVTPDKWPQWPVKAGYLTPRGAGLVTLMGGFYGDYFRSYGLLPAGCPADESIYVQADVDQRTRLTGQAFLDGIAPDCGLKVHYQADLKKIDPLFHTVEAGVCKLDPEKTHQAVEKRLGGPLNELSQRYAKPFALMGEVLNFSASPYCNSLQQKGKACDFATFAANEIEVNKEGTKVSLSGPLALSSTLGEIFLLQNSQAMPDVAWNRLSGEENWISLLSLHNAQFDLMAKTPYIARHKGTPLLQQIDTALVLQRDAQGQTLPLSPQTKLLFLGGHDTNIANIAGMLGANWQLPQQPDNTPPGGGLVFELWQNPDNHQRYVAVKMFYQTMEQLRNADKLDLKNNPARIVPIAIEGCENEGDNKLCQLETFQKKVAQVIEPSCHI 414
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405

Chain B from PDB  Type:PROTEIN  Length:409
 aligned with H9TUK6_YERKR | H9TUK6 from UniProtKB/TrEMBL  Length:441

    Alignment length:409
                                    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       302       312       322       332       342       352       362       372       382       392       402       412       422       432         
         H9TUK6_YERKR    33 GYTLERVVILSRHGVRSPTKQTQLMNDVTPDKWPQWPVKAGYLTPRGAGLVTLMGGFYGDYFRSYGLLPAGCPADESIYVQADVDQRTRLTGQAFLDGIAPDCGLKVHYQADLKKIDPLFHTVEAGVCKLDPEKTHQAVEKRLGGPLNELSQRYAKPFALMGEVLNFSASPYCNSLQQKGKACDFATFAANEIEVNKEGTKVSLSGPLALSSTLGEIFLLQNSQAMPDVAWNRLSGEENWISLLSLHNAQFDLMAKTPYIARHKGTPLLQQIDTALVLQRDAQGQTLPLSPQTKLLFLGGHDTNIANIAGMLGANWQLPQQPDNTPPGGGLVFELWQNPDNHQRYVAVKMFYQTMEQLRNADKLDLKNNPARIVPIAIEGCENEGDNKLCQLETFQKKVAQVIEPSCHI 441
               SCOP domains d4arvb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.........hhhhhhh...............hhhhhhhhhhhhhhhhhhhhhh............eeeee..hhhhhhhhhhhhhhhh..............................hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh...eeee......eeeehhhhhhhhhhhhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................eeeeeehhhhhhhhhhhhh................eeeeeeee......eeeeeeeee.hhhhhhhh..........eeee..............eehhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4arv B   6 GYTLERVVILSRHGVRSPTKQTQLMNDVTPDKWPQWPVKAGYLTPRGAGLVTLMGGFYGDYFRSYGLLPAGCPADESIYVQADVDQRTRLTGQAFLDGIAPDCGLKVHYQADLKKIDPLFHTVEAGVCKLDPEKTHQAVEKRLGGPLNELSQRYAKPFALMGEVLNFSASPYCNSLQQKGKACDFATFAANEIEVNKEGTKVSLSGPLALSSTLGEIFLLQNSQAMPDVAWNRLSGEENWISLLSLHNAQFDLMAKTPYIARHKGTPLLQQIDTALVLQRDAQGQTLPLSPQTKLLFLGGHDTNIANIAGMLGANWQLPQQPDNTPPGGGLVFELWQNPDNHQRYVAVKMFYQTMEQLRNADKLDLKNNPARIVPIAIEGCENEGDNKLCQLETFQKKVAQVIEPSCHI 414
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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) (23833)

Fold: Phosphoglycerate mutase-like (103)

Superfamily: Phosphoglycerate mutase-like (103)

Family: automated matches (13)

Protein domain: automated matches (13)

Yersinia kristensenii [TaxId: 28152] (1)

1a	d4arva_	A:
1b	d4arvb_	B:

(no "CATH Domain" information available for 4ARV)

(no "Pfam Domain" information available for 4ARV)

Asymmetric Unit(hide GO term definitions)

Chain A,B (H9TUK6_YERKR | H9TUK6)

molecular function
	GO:0003993	acid phosphatase activity	Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an acid pH optimum.
biological process
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.

Asymmetric Unit
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	Cis Peptide Bonds
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Biological Units
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4aro	HAFNIA ALVEI PHYTASE IN COMPLEX WITH MYO-INOSITOL HEXAKIS SULPHATE
4ars	HAFNIA ALVEI PHYTASE APO FORM
4aru	HAFNIA ALVEI PHYTASE IN COMPLEX WITH TARTRATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 12)

Sites (12, 12)

SS Bonds (8, 8)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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