2Q3U - JenaLib

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Title :   ENSEMBLE REFINEMENT OF THE PROTEIN CRYSTAL STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT5G08170, AGMATINE IMINOHYDROLASE

Authors :   E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips Jr. , Cent Eukaryotic Structural Genomics (Cesg)

Date :   30 May 07 (Deposition) - 19 Jun 07 (Release) - 10 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.53

Chains :   Asym. Unit : A,B  (8x)
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Ensemble Refinement, Refinement Methodology Development, At5G08170, Polyamine Biosynthesis, Agmatine Iminohydrolase, Aih, Agmatine Deiminase, N-Carbamoylputrescine, Putrescine, Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips
Ensemble Refinement Of Protein Crystal Structures: Validation And Application.
Structure V. 15 1040 2007
PubMed-ID: 17850744 | Reference-DOI: 10.1016/J.STR.2007.06.019

Molecule 1 - AGMATINE DEIMINASE
	Chains	:	A, B
	EC Number	:	3.5.3.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PVP13
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AIH, AT5G08170, T22D6.110
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Strain	:	CV. COLUMBIA
	Synonym	:	AGMATINE IMINOHYDROLASE

		1	2
Asymmetric Unit (8x)	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 30)

No.	Name	Count	Type	Full Name
1	EDO	13	Ligand/Ion	1,2-ETHANEDIOL
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	MPO	1	Ligand/Ion	3[N-MORPHOLINO]PROPANE SULFONIC ACID
4	MSE	14	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (3, 15)

No.	Name	Count	Type	Full Name
1	EDO	7	Ligand/Ion	1,2-ETHANEDIOL
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MPO	1	Ligand/Ion	3[N-MORPHOLINO]PROPANE SULFONIC ACID
4	MSE	7	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 13)

No.	Name	Count	Type	Full Name
1	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MPO	-1	Ligand/Ion	3[N-MORPHOLINO]PROPANE SULFONIC ACID
4	MSE	7	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP B:119 , TRP B:120 , SER B:143 , HOH B:929 , HOH B:944 , HOH B:987	BINDING SITE FOR RESIDUE MG B 801
02	AC2	SOFTWARE	ASP A:119 , TRP A:120 , SER A:143 , HOH A:1040 , HOH A:1055 , HOH A:1180	BINDING SITE FOR RESIDUE MG A 802
03	AC3	SOFTWARE	ASN A:35 , ASP A:89 , TRP A:91 , TRP A:125 , CYS A:132 , THR A:221 , ARG A:301 , ALA A:360 , HOH A:1225	BINDING SITE FOR RESIDUE EDO A 901
04	AC4	SOFTWARE	ARG A:337 , ASP A:341 , HOH A:1077	BINDING SITE FOR RESIDUE EDO A 902
05	AC5	SOFTWARE	TRP A:91 , ASP A:94 , TRP A:125 , GLY A:361 , GLY A:362 , HOH A:1383	BINDING SITE FOR RESIDUE EDO A 903
06	AC6	SOFTWARE	TRP B:91 , ASP B:94 , GLY B:361 , GLY B:362 , CYS B:366 , HOH B:983	BINDING SITE FOR RESIDUE EDO B 904
07	AC7	SOFTWARE	TRP B:19 , ARG B:233 , HIS B:346	BINDING SITE FOR RESIDUE EDO B 905
08	AC8	SOFTWARE	ASN A:123 , GLY A:126 , ILE A:160 , LYS A:184 , ASN A:185 , ARG A:186 , PRO A:188	BINDING SITE FOR RESIDUE EDO A 906
09	AC9	SOFTWARE	TYR A:216 , GLY A:217 , ASP A:218 , GLU A:219 , ARG A:252 , HOH A:1064	BINDING SITE FOR RESIDUE EDO A 907
10	BC1	SOFTWARE	GLU A:84 , HOH A:1038 , GLU B:84 , LEU B:149 , HOH B:993	BINDING SITE FOR RESIDUE EDO A 908
11	BC2	SOFTWARE	SER B:55 , PHE B:57 , GLU B:58 , PRO B:59 , HOH B:1148 , HOH B:1149	BINDING SITE FOR RESIDUE EDO B 909
12	BC3	SOFTWARE	THR A:246 , TYR A:283	BINDING SITE FOR RESIDUE EDO A 910
13	BC4	SOFTWARE	TRP B:125 , ASP B:130 , CYS B:132 , ASN B:185 , GLU B:219 , ASP B:220 , ASN B:222	BINDING SITE FOR RESIDUE EDO B 911
14	BC5	SOFTWARE	SER B:7 , ARG B:154 , GLN B:156 , HOH B:965	BINDING SITE FOR RESIDUE EDO B 912
15	BC6	SOFTWARE	TYR B:14 , PRO B:16 , ASP B:20 , ALA B:373 , HOH B:972	BINDING SITE FOR RESIDUE EDO B 913
16	BC7	SOFTWARE	TYR A:14 , GLY A:172 , GLY A:204 , GLN A:206 , HOH A:1051	BINDING SITE FOR RESIDUE MPO A 9000

(no "SS Bond" information available for 2Q3U)

(no "Cis Peptide Bond" information available for 2Q3U)

(no "SAP(SNP)/Variant" information available for 2Q3U)

(no "PROSITE Motif" information available for 2Q3U)

(no "Exon" information available for 2Q3U)

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:365
 aligned with AGUA_ARATH | Q8GWW7 from UniProtKB/Swiss-Prot  Length:383

    Alignment length:372
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374  
           AGUA_ARATH     5 RESPAEHGYYMPAEWDSHAQTWIGWPERQDNWRHNALPAQRVFADVAKAISKFEPVTVCASPAQWENARKQLPEDIRVVEMSMNDSWFRDSGPTFIVRKRPVKLSSLNRNIAGIDWNFNAWGGANDGCYNDWSHDLLVSRKILALERIPRFQHSMILEGGSIHVDGEGTCLVTEECLLNKNRNPHMSKEQIEEELKKYLGVQSFIWLPRGLYGDEDTNGHIDNMCCFARPGVVLLSWTDDETDPQYERSVEALSVLSNSIDARGRKIQVIKLYIPEPLYMTEEESSGITQDGEAIPRLAGTRLAASYVNFYIANGGIIAPQFGDPIRDKEAIRVLSDTFPHHSVVGIENAREIVLAGGNIHCITQQQPAEPT 376
               SCOP domains d2q3ua_ A: automated matches                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2q3uA00 A:5-376 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhh.ee.......eeeeee.........hhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhh....eeee......hhhhhh.eeeee..-------...eeeeeee................hhhhhhhhhhhhhh..eeeeeee.hhh.eee....eeeeehhhhh........hhhhhhhhhhhhhh..eeeee............hhhh.eeeee..eeeeee......hhhhhhhhhhhhhhh.........eeeeee.......hhhhhh........................eee..eeeee...hhhhhhhhhhhhhh.....eeeee..hhhhhh....hhh.eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2q3u A   5 RESPAEHGYYmPAEWDSHAQTWIGWPERQDNWRHNALPAQRVFAGVAKAISKFEPVTVCASPAQWENARKQLPEDIRVVEmSmNDSWFRDSGPTFIVRKR-------NRNIAGIDWNFNAWGGANDGCYNDWSHDLLVSRKILALERIPRFQHSmILEGGSIHVDGEGTCLVTEECLLNKNRNPHmSKEQIEEELKKYLGVQSFIWLPRGLYGDEDTNGHIDNmCCFARPGVVLLSWTDDETDPQYERSVEALSVLSNSIDARGRKIQVIKLYIPEPLYmTEEESSGITQDGEAIPRLAGTRLAASYVNFYIANGGIIAPQFGDPIRDKEAIRVLSDTFPHHSVVGIENAREIVLAGGNIHCITQQQPAEPT 376
                                    14|       24        34        44        54        64        74        84| |     94       104       114       124       134       144       154    |  164       174       184     | 194       204       214       224   |   234       244       254       264       274       284       294       304       314       324       334       344       354       364       374  
                                     15-MSE                                                                85-MSE            104     112                                            159-MSE                        190-MSE                               228-MSE                                                 284-MSE                                                                                        
                                                                                                             87-MSE

Chain B from PDB  Type:PROTEIN  Length:363
 aligned with AGUA_ARATH | Q8GWW7 from UniProtKB/Swiss-Prot  Length:383

    Alignment length:370
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376
           AGUA_ARATH     7 SPAEHGYYMPAEWDSHAQTWIGWPERQDNWRHNALPAQRVFADVAKAISKFEPVTVCASPAQWENARKQLPEDIRVVEMSMNDSWFRDSGPTFIVRKRPVKLSSLNRNIAGIDWNFNAWGGANDGCYNDWSHDLLVSRKILALERIPRFQHSMILEGGSIHVDGEGTCLVTEECLLNKNRNPHMSKEQIEEELKKYLGVQSFIWLPRGLYGDEDTNGHIDNMCCFARPGVVLLSWTDDETDPQYERSVEALSVLSNSIDARGRKIQVIKLYIPEPLYMTEEESSGITQDGEAIPRLAGTRLAASYVNFYIANGGIIAPQFGDPIRDKEAIRVLSDTFPHHSVVGIENAREIVLAGGNIHCITQQQPAEPT 376
               SCOP domains d2q3ub_ B: automated matches                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2q3uB00 B:7-376 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) ------PAD_porph-2q3uB01 B:13-372                                                                                                                                                                                                                                                                                                                                              ---- Pfam domains (1)
           Pfam domains (2) ------PAD_porph-2q3uB02 B:13-372                                                                                                                                                                                                                                                                                                                                              ---- Pfam domains (2)
         Sec.struct. author hhhhhh.........eeeeee.........hhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhh....eeee......hhhhhh.eeee...-------...eeeeeee................hhhhhhhhhhhhhh..eeeeeee.hhhhhee....eeeeehhhhh........hhhhhhhhhhhhh...eeeee............hhhh.eeeee..eeeeee.....hhhhhhhhhhhhhhhh.........eeeeee.......hhhhhhh.......................eee..eeeee...hhhhhhhhhhhhhhhh...eeeee.hhhhhhh...hhhhheeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q3u B   7 SPAEHGYYmPAEWDSHAQTWIGWPERQDNWRHNALPAQRVFAGVAKAISKFEPVTVCASPAQWENARKQLPEDIRVVEmSmNDSWFRDSGPTFIVRKR-------NRNIAGIDWNFNAWGGANDGCYNDWSHDLLVSRKILALERIPRFQHSmILEGGSIHVDGEGTCLVTEECLLNKNRNPHmSKEQIEEELKKYLGVQSFIWLPRGLYGDEDTNGHIDNmCCFARPGVVLLSWTDDETDPQYERSVEALSVLSNSIDARGRKIQVIKLYIPEPLYmTEEESSGITQDGEAIPRLAGTRLAASYVNFYIANGGIIAPQFGDPIRDKEAIRVLSDTFPHHSVVGIENAREIVLAGGNIHCITQQQPAEPT 376
                                    16        26        36        46        56        66        76        86|       96       | -     | 116       126       136       146       156  |    166       176       186   |   196       206       216       226 |     236       246       256       266       276       286       296       306       316       326       336       346       356       366       376
                                   15-MSE                                                                85-MSE            104     112                                            159-MSE                        190-MSE                               228-MSE                                                 284-MSE                                                                                        
                                                                                                           87-MSE

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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) (23004)

Fold: Pentein, beta/alpha-propeller (68)

Superfamily: Pentein (68)

Family: Porphyromonas-type peptidylarginine deiminase (10)

Protein domain: automated matches (3)

Thale cress (Arabidopsis thaliana) [TaxId: 3702] (3)

1a	d2q3ua_	A:
1b	d2q3ub_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 5-stranded Propeller (36)

Topology: L-arginine/glycine Amidinotransferase; Chain A (36)

Homologous Superfamily: L-arginine/glycine Amidinotransferase; Chain A (33)

Thale cress (Arabidopsis thaliana) (2)

1a	2q3uB00	B:7-376
1b	2q3uA00	A:5-376

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GME (20)

Family: PAD_porph (5)

Arabidopsis thaliana (Mouse-ear cress) (2)

1a	PAD_porph-2q3uB01	B:13-372
1b	PAD_porph-2q3uB02	B:13-372

Asymmetric Unit(hide GO term definitions)

Chain A,B (AGUA_ARATH | Q8GWW7)

molecular function
	GO:0047632	agmatine deiminase activity	Catalysis of the reaction: agmatine + H2O = N-carbamoylputrescine + NH3.
	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:0004668	protein-arginine deiminase activity	Catalysis of the reaction: protein L-arginine + H2O = protein L-citrulline + NH3.
biological process
	GO:0006596	polyamine biosynthetic process	The chemical reactions and pathways resulting in the formation of polyamines, any organic compound containing two or more amino groups.
	GO:0009446	putrescine biosynthetic process	The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane; putrescine can be synthesized from arginine or ornithine and is the metabolic precursor of spermidine and spermine.
	GO:0033388	putrescine biosynthetic process from arginine	The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from other compounds, including arginine.

Asymmetric Unit
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	2q3u
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	AGUA_ARATH \| Q8GWW7	:	1vkp 3h7c 3h7k

1vkp	ORIGINAL REFINEMENT BASED ON SAME DATA AND R-FREE SET.

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Ligands, Modified Residues, Ions (4, 30)

Sites (16, 16)

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