1RKQ - JenaLib

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Title :   CRYSTAL STRUCTURE OF HAD-LIKE PHOSPHATASE YIDA FROM E. COLI

Authors :   U. A. Ramagopal, S. C. Almo, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   23 Nov 03 (Deposition) - 09 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Two Domain Structure With Beta-Alpha Sandwich. Stucture Contains A Magnesium Ion. , Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   U. A. Ramagopal, S. C. Almo
Crystal Structure Of Nysgrc Target T1436: A Hypothetical Protein Yida.
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL PROTEIN YIDA
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	YIDA, B3697, C4619, SF3767, S4004
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		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 (2, 4)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:10 , GLY A:45 , LYS A:198 , ASN A:224 , HOH A:1276	BINDING SITE FOR RESIDUE CL A 1272
2	AC2	SOFTWARE	ASP B:10 , GLY B:45 , LYS B:198 , ASN B:224 , HOH B:2276	BINDING SITE FOR RESIDUE CL B 2272
3	AC3	SOFTWARE	ASP A:10 , ASP A:12 , ASP A:221 , HOH A:1274 , HOH A:1275 , HOH A:1276	BINDING SITE FOR RESIDUE MG A 1273
4	AC4	SOFTWARE	ASP B:10 , ASP B:12 , ASP B:221 , HOH B:2274 , HOH B:2275 , HOH B:2276	BINDING SITE FOR RESIDUE MG B 2273

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

(no "Cis Peptide Bond" information available for 1RKQ)

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COF_1	PS01228	Hypothetical cof family signature 1.	YIDA_ECOLI	5-16	2	A:6-17 B:6-17
2	COF_2	PS01229	Hypothetical cof family signature 2.	YIDA_ECOLI	218-240	2	A:219-241 B:219-241

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COF_1	PS01228	Hypothetical cof family signature 1.	YIDA_ECOLI	5-16	1	A:6-17 -
2	COF_2	PS01229	Hypothetical cof family signature 2.	YIDA_ECOLI	218-240	1	A:219-241 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COF_1	PS01228	Hypothetical cof family signature 1.	YIDA_ECOLI	5-16	1	- B:6-17
2	COF_2	PS01229	Hypothetical cof family signature 2.	YIDA_ECOLI	218-240	1	- B:219-241

(no "Exon" information available for 1RKQ)

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:271
 aligned with YIDA_ECOLI | P0A8Y5 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:271
                             1                                                                                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269 
           YIDA_ECOLI     - -MAIKLIAIDMDGTLLLPDHTISPAVKNAIAAARARGVNVVLTTGRPYAGVHNYLKELHMEQPGDYCITYNGALVQKAADGSTVAQTALSYDDYRFLEKLSREVGSHFHALDRTTLYTANRDISYYTVHESFVATIPLVFCEAEKMDPNTQFLKVMMIDEPAILDQAIARIPQEVKEKYTVLKSAPYFLEILDKRVNKGTGVKSLADVLGIKPEEIMAIGDQENDIAMIEYAGVGVAMDNAIPSVKEVANFVTKSNLEDGVAFAIEKYVLN 270
               SCOP domains d1rkqa_ A: Hypothetical protein YidA                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1rkqA01 A:1-87,A:195-271  [code=3.40.50.1000, no name defined]                         1rkqA02 A:88-194  [code=3.30.1240.10, no name defined]                                                     1rkqA01 A:1-87,A:195-271  [code=3.40.50.1000, no name defined]                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.............hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh.......eeeehhh.eeee.....eeee...hhhhhhhhhhhhhhhh.eeeee....eee.....hhhhhhhhhhh...eee.hhhhh.......eeeee.hhhhhhhhhhhhhhhhhhheeeeeee..eeeeee...hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeee....hhhhhhhh.ee......hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----COF_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COF_2  PDB: A:219-241  ------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rkq A   1 SLAIKLIAIDMDGTLLLPDHTISPAVKNAIAAARARGVNVVLTTGRPYAGVHNYLKELHMEQPGDYCITYNGALVQKAADGSTVAQTALSYDDYRFLEKLSREVGSHFHALDRTTLYTANRDISYYTVHESFVATIPLVFCEAEKMDPNTQFLKVMMIDEPAILDQAIARIPQEVKEKYTVLKSAPYFLEILDKRVNKGTGVKSLADVLGIKPEEIMAIGDQENDIAMIEYAGVGVAVDNAIPSVKEVANFVTKSNLEDGVAFAIEKYVLN 271
                                    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       270

Chain B from PDB  Type:PROTEIN  Length:271
 aligned with YIDA_ECOLI | P0A8Y5 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:271
                             1                                                                                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269 
           YIDA_ECOLI     - -MAIKLIAIDMDGTLLLPDHTISPAVKNAIAAARARGVNVVLTTGRPYAGVHNYLKELHMEQPGDYCITYNGALVQKAADGSTVAQTALSYDDYRFLEKLSREVGSHFHALDRTTLYTANRDISYYTVHESFVATIPLVFCEAEKMDPNTQFLKVMMIDEPAILDQAIARIPQEVKEKYTVLKSAPYFLEILDKRVNKGTGVKSLADVLGIKPEEIMAIGDQENDIAMIEYAGVGVAMDNAIPSVKEVANFVTKSNLEDGVAFAIEKYVLN 270
               SCOP domains d1rkqb_ B: Hypothetical protein YidA                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1rkqB01 B:1-87,B:195-271  [code=3.40.50.1000, no name defined]                         1rkqB02 B:88-194  [code=3.30.1240.10, no name defined]                                                     1rkqB01 B:1-87,B:195-271  [code=3.40.50.1000, no name defined]                CATH domains
           Pfam domains (1) ------Hydrolase_3-1rkqB01 B:7-265                                                                                                                                                                                                                                        ------ Pfam domains (1)
           Pfam domains (2) ------Hydrolase_3-1rkqB02 B:7-265                                                                                                                                                                                                                                        ------ Pfam domains (2)
         Sec.struct. author .....eeee.............hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh.......eeeehhh.eeee.....eeee...hhhhhhhhhhhhhhhh.eeeee....eee.....hhhhhhhhhhh...eee.hhhhh.......eeeee.hhhhhhhhhhh.hhhhhhheeeeeee..eeeeee...hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeee....hhhhhh...ee......hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----COF_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COF_2  PDB: B:219-241  ------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rkq B   1 SLAIKLIAIDMDGTLLLPDHTISPAVKNAIAAARARGVNVVLTTGRPYAGVHNYLKELHMEQPGDYCITYNGALVQKAADGSTVAQTALSYDDYRFLEKLSREVGSHFHALDRTTLYTANRDISYYTVHESFVATIPLVFCEAEKMDPNTQFLKVMMIDEPAILDQAIARIPQEVKEKYTVLKSAPYFLEILDKRVNKGTGVKSLADVLGIKPEEIMAIGDQENDIAMIEYAGVGVAVDNAIPSVKEVANFVTKSNLEDGVAFAIEKYVLN 271
                                    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       270

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) (23833)

Fold: HAD-like (349)

Superfamily: HAD-like (349)

Family: Predicted hydrolases Cof (35)

Protein domain: Hypothetical protein YidA (1)

Escherichia coli [TaxId: 562] (1)

1a	d1rkqa_	A:
1b	d1rkqb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 (8)

Homologous Superfamily: [code=3.30.1240.10, no name defined] (8)

Escherichia coli. Organism_taxid: 562. (4)

1a	1rkqA02	A:88-194
1b	1rkqB02	B:88-194

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1000, no name defined] (211)

Escherichia coli. Organism_taxid: 562. (14)

2a	1rkqA01	A:1-87,A:195-271
2b	1rkqB01	B:1-87,B:195-271

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HAD (186)

Family: Hydrolase_3 (28)

Escherichia coli (strain K12) (4)

1a	Hydrolase_3-1rkqB01	B:7-265
1b	Hydrolase_3-1rkqB02	B:7-265

Asymmetric Unit(hide GO term definitions)

Chain A,B (YIDA_ECOLI | P0A8Y5)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0050308	sugar-phosphatase activity	Catalysis of the reaction: sugar phosphate + H2O = sugar + phosphate.
biological process
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0044283	small molecule biosynthetic process	The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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