2Q4E - JenaLib

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Title :   ENSEMBLE REFINEMENT OF THE PROTEIN CRYSTAL STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT4G09670

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

Date :   31 May 07 (Deposition) - 19 Jun 07 (Release) - 10 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.49

Chains :   Asym. Unit : A,B  (16x)
Biol. Unit 1: A,B  (1x)

Keywords :   Ensemble Refinement, Refinement Methodology Development, At4G09670, Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Oxidoreductase (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 - PROBABLE OXIDOREDUCTASE AT4G09670
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PVP-17
	Expression System Strain	:	B834 P(RARE2)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AT4G09670, F17A8.20
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Strain	:	CV. COLUMBIA

		1	2
Asymmetric Unit (16x)	:	A	B
Biological Unit 1 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 12)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 12)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2Q4E)

(no "SS Bond" information available for 2Q4E)

Asymmetric Unit

No.	Model	Residues
1	1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16	Lys A:102	-	Pro A:103
2	1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16	Ala B:28	-	Pro B:29
3	1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16	Lys B:102	-	Pro B:103

(no "SAP(SNP)/Variant" information available for 2Q4E)

(no "PROSITE Motif" information available for 2Q4E)

(no "Exon" information available for 2Q4E)

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:343
 aligned with Y4967_ARATH | Q9SZ83 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:355
                                    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     
          Y4967_ARATH     6 QIRIGVMGCADIARKVSRAIHLAPNATISGVASRSLEKAKAFATANNYPESTKIHGSYESLLEDPEIDALYVPLPTSLHVEWAIKAAEKGKHILLEKPVAMNVTEFDKIVDACEANGVQIMDGTMWVHNPRTALLKEFLSDSERFGQLKTVQSCFSFAGDEDFLKNDIRVKPGLDGLGALGDAGWYAIRATLLANNFELPKTVTAFPGAVLNEAGVILSCGASLSWEDGRTATIYCSFLANLTMEITAIGTKGTLRVHDFIIPYKETEASFTTSTKAWFNDLVTAWVSPPSEHTVKTELPQEACMVREFARLVGEIKNNGAKPDGYWPSISRKTQLVVDAVKESVDKNYQQISLS 360
               SCOP domains d2q4ea1 A:6-133,A:305-360 Probable oxidoreductase At4g09670                                                                     d2q4ea2 A:134-304 Probable oxidoreductase At4g09670                                                                                                                        d2q4ea1 A:6-13            3,A:305-360                    SCOP domains
               CATH domains 2q4eA01 A:6-133 NAD(P)-binding Rossmann-like Domain                                                                             ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh......ee..hhhhhhh.....eeee..hhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhh...eee..hhhhhhhhh..............eeeeeeeee...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.........ee....ee.....eeeeeee.......eeeeeee......eeeeeee..eeeee..........ee..eeee...............ee..ee...hhhhhhhhhhh...------------hhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q4e A   6 QIRIGVmGCADIARKVSRAIHLAPNATISGVASRSLEKAKAFATANNYPESTKIHGSYESLLEDPEIDALYVPLPTSLHVEWAIKAAEKGKHILLEKPVAmNVTEFDKIVDACEANGVQImDGTmWVHNPRTALLKEFLSDSERFGQLKTVQSCFSFAGDEDFLKNDIRVKPGLDGLGALGDAGWYAIRATLLANNFELPKTVTAFPGAVLNEAGVILSCGASLSWEDGRTATIYCSFLANLTmEITAIGTKGTLRVHDFIIPYKETEASFTTSTKAWFNDLVTAWVSPPSEHTVKTELPQEACmVREFARLV------------YWPSISRKTQLVVDAVKESVDKNYQQISLS 360
                                  | 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  |      -     | 335       345       355     
                                 12-MSE                                                                                       106-MSE             126-MSE                                                                                                                    249-MSE                                                      310-MSE 318          331                             
                                                                                                                                                      130-MSE

Chain B from PDB  Type:PROTEIN  Length:350
 aligned with Y4967_ARATH | Q9SZ83 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:355
                                    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     
          Y4967_ARATH     6 QIRIGVMGCADIARKVSRAIHLAPNATISGVASRSLEKAKAFATANNYPESTKIHGSYESLLEDPEIDALYVPLPTSLHVEWAIKAAEKGKHILLEKPVAMNVTEFDKIVDACEANGVQIMDGTMWVHNPRTALLKEFLSDSERFGQLKTVQSCFSFAGDEDFLKNDIRVKPGLDGLGALGDAGWYAIRATLLANNFELPKTVTAFPGAVLNEAGVILSCGASLSWEDGRTATIYCSFLANLTMEITAIGTKGTLRVHDFIIPYKETEASFTTSTKAWFNDLVTAWVSPPSEHTVKTELPQEACMVREFARLVGEIKNNGAKPDGYWPSISRKTQLVVDAVKESVDKNYQQISLS 360
               SCOP domains d2q4eb1 B:6-133,B:305-360 Probable oxidoreductase At4g09670                                                                     d2q4eb2 B:134-304 Probable oxidoreductase At4g09670                                                                                                                        d2q4eb1 B:6     -133,B:305-360                           SCOP domains
               CATH domains 2q4eB01 B:6-133 NAD(P)-binding Rossmann-like Domain                                                                             ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -GFO_IDH_MocA-2q4eB01 B:7-129                                                                                               -----------GFO_IDH_MocA_C-2q4eB03 B:141-254                                                                                  ---------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -GFO_IDH_MocA-2q4eB02 B:7-129                                                                                               -----------GFO_IDH_MocA_C-2q4eB04 B:141-254                                                                                  ---------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeee....hhhhhhhhhhh....eeeeee...hhhhhhhhhhhh......ee..hhhhhhh.....eeee..hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhh......eeeeeeeeeee.hhhhhhhh..........hhhhhhhhhhhhhhhhhh......eeee....ee.....eeeeeeeee.....eeeeeee.eeeeeeeeeeee..eeeee..........eeeeeeee...............eeeeee...hhhhhhhhhhh-----.........hhhhhhhhhhhhhhhhhhhhhh....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q4e B   6 QIRIGVmGCADIARKVSRAIHLAPNATISGVASRSLEKAKAFATANNYPESTKIHGSYESLLEDPEIDALYVPLPTSLHVEWAIKAAEKGKHILLEKPVAmNVTEFDKIVDACEANGVQImDGTmWVHNPRTALLKEFLSDSERFGQLKTVQSCFSFAGDEDFLKNDIRVKPGLDGLGALGDAGWYAIRATLLANNFELPKTVTAFPGAVLNEAGVILSCGASLSWEDGRTATIYCSFLANLTmEITAIGTKGTLRVHDFIIPYKETEASFTTSTKAWFNDLVTAWVSPPSEHTVKTELPQEACmVREFA-----IKNNGAKPDGYWPSISRKTQLVVDAVKESVDKNYQQISLS 360
                                  | 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     
                                 12-MSE                                                                                       106-MSE             126-MSE                                                                                                                    249-MSE                                                      310-MSE5   321                                       
                                                                                                                                                      130-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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Thale cress (Arabidopsis thaliana) (15)

1a	2q4eA01	A:6-133
1b	2q4eB01	B:6-133

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: GFO_IDH_MocA (25)

Arabidopsis thaliana (Mouse-ear cress) (1)

1a	GFO_IDH_MocA-2q4eB01	B:7-129
1b	GFO_IDH_MocA-2q4eB02	B:7-129

Clan: ox_reductase_C (19)

Family: GFO_IDH_MocA_C (19)

Arabidopsis thaliana (Mouse-ear cress) (1)

2a	GFO_IDH_MocA_C-2q4eB03	B:141-254
2b	GFO_IDH_MocA_C-2q4eB04	B:141-254

Asymmetric Unit(hide GO term definitions)

Chain A,B (Y4967_ARATH | Q9SZ83)

molecular function
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
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.

Asymmetric Unit
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	Sites
(no "Sites" information available for 2q4e)

	Cis Peptide Bonds
		Ala B:28 - Pro B:29	[ RasMol ]
		Lys A:102 - Pro A:103	[ RasMol ]
		Lys B:102 - Pro B:103	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	Y4967_ARATH \| Q9SZ83	:	1ydw

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

Description

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Ligands, Modified Residues, Ions (1, 12)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 48)

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