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(-) Description

Title :  CRYSTAL STRUCTURE OF A SAM DEPENDENT METHYL-TRANSFERASE TYPE 12 FAMILY PROTEIN (ECA1738) FROM PECTOBACTERIUM ATROSEPTICUM SCRI1043 AT 1.85 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  20 Mar 07  (Deposition) - 03 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B,C,D  (4x)
Biol. Unit 3:  A (2x),B (2x),C (2x),D (2x)
Keywords :  Putative Methyltransferase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Hypothetical Protein (Yp_049838. 1) Fro Erwinia Carotovora Atroseptica Scri1043 At 1. 85 A Resolutio
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN
    AtccBAA-672
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidSPEEDET
    Expression System StrainHK100
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneYP_049838.1, ECA1738
    Organism ScientificPECTOBACTERIUM ATROSEPTICUM SCRI1043
    Organism Taxid218491
    StrainSCRI 1043

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)ABCD
Biological Unit 2 (4x)ABCD
Biological Unit 3 (2x)A (2x)B (2x)C (2x)D (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 30)

Asymmetric Unit (5, 30)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2EDO7Ligand/Ion1,2-ETHANEDIOL
3MSE12Mod. Amino AcidSELENOMETHIONINE
4NA2Ligand/IonSODIUM ION
5TRS4Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (3, 23)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO7Ligand/Ion1,2-ETHANEDIOL
3MSE12Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION
5TRS4Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (3, 92)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO28Ligand/Ion1,2-ETHANEDIOL
3MSE48Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION
5TRS16Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 3 (3, 26)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO10Ligand/Ion1,2-ETHANEDIOL
3MSE12Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION
5TRS4Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA B:131 , GLU B:132 , HOH B:268BINDING SITE FOR RESIDUE CL B 251
02AC2SOFTWARECYS A:174 , ARG A:183 , HOH A:263 , HOH A:286BINDING SITE FOR RESIDUE CL A 250
03AC3SOFTWAREALA D:131 , GLU D:132 , HOH D:275BINDING SITE FOR RESIDUE CL D 250
04AC4SOFTWAREASN C:248 , GLN C:249 , HIS D:114 , ASP D:116 , HOH D:277 , HOH D:279BINDING SITE FOR RESIDUE NA D 251
05AC5SOFTWAREASN A:248 , GLN A:249 , HIS B:114 , ASP B:116 , HOH B:270 , HOH B:292BINDING SITE FOR RESIDUE NA B 252
06AC6SOFTWAREGLU B:47 , GLY B:49 , PHE B:55 , THR B:109 , HOH B:263 , HOH B:273BINDING SITE FOR RESIDUE TRS B 253
07AC7SOFTWAREGLU A:47 , GLY A:49 , PHE A:55 , THR A:109 , VAL A:111 , HOH A:269 , HOH A:305 , HOH A:340 , HOH A:395 , HOH A:419BINDING SITE FOR RESIDUE TRS A 251
08AC8SOFTWAREGLU C:47 , GLY C:49 , PHE C:55 , THR C:109 , VAL C:111 , HOH C:260 , HOH C:278 , HOH C:313 , HOH C:405BINDING SITE FOR RESIDUE TRS C 251
09AC9SOFTWAREGLU D:47 , GLY D:49 , PHE D:55 , THR D:109 , HOH D:265 , HOH D:291 , HOH D:417BINDING SITE FOR RESIDUE TRS D 252
10BC1SOFTWARELEU D:99 , ARG D:101 , ARG D:102 , ASP D:128 , TRP D:129 , HOH D:283 , HOH D:330 , HOH D:370BINDING SITE FOR RESIDUE EDO D 253
11BC2SOFTWAREARG B:41 , HIS B:62 , PHE B:63 , HOH B:372BINDING SITE FOR RESIDUE EDO B 254
12BC3SOFTWAREHIS D:159 , SER D:161 , HOH D:312 , HOH D:364BINDING SITE FOR RESIDUE EDO D 254
13BC4SOFTWAREPRO A:141 , ARG A:148 , GLU A:167 , HIS A:172 , THR A:175 , HOH A:262 , HOH A:278BINDING SITE FOR RESIDUE EDO A 252
14BC5SOFTWAREPRO C:141 , ARG C:148 , GLU C:167 , HIS C:172 , THR C:175 , HOH C:256 , HOH C:277 , HOH C:326 , HOH C:382BINDING SITE FOR RESIDUE EDO C 252
15BC6SOFTWAREPRO D:141 , ARG D:148 , HIS D:172 , THR D:175 , HOH D:269 , HOH D:299 , HOH D:358BINDING SITE FOR RESIDUE EDO D 255
16BC7SOFTWAREPRO B:141 , ARG B:148 , GLU B:167 , HIS B:172 , THR B:175 , HOH B:261 , HOH B:284 , HOH B:331BINDING SITE FOR RESIDUE EDO B 255

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P7H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2P7H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P7H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P7H)

(-) Exons   (0, 0)

(no "Exon" information available for 2P7H)

(-) Sequences/Alignments

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:229
 aligned with Q6D6E7_PECAS | Q6D6E7 from UniProtKB/TrEMBL  Length:249

    Alignment length:229
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
         Q6D6E7_PECAS    21 YNFDFDVMHPFMVRAFTPFFRPGNLLELGSFKGDFTSRLQEHFNDITCVEASEEAISHAQGRLKDGITYIHSRFEDAQLPRRYDNIVLTHVLEHIDDPVALLKRINDDWLAEGGRLFLVCPNANAVSRQIAVKMGIISHNSAVTEAEFAHGHRCTYALDTLERDASRAGLQVTYRSGIFFKALANFQWDQILQTDILSKEYLDGCYQLGQQYPDLCASIFLLCEKGINQ 249
               SCOP domains d2p7ha1 A:21-249 Hypothetical protein ECA1738                                                                                                                                                                                         SCOP domains
               CATH domains 2p7hA00 A:21-249 Vaccinia Virus protein VP39                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhh.....eeeee.hhhhhhhhhhhh...eeeee...........eeeeeee.hhhhh.hhhhhhhhhhhhheeeeeeeeeeee...hhhhhhhhhh.........hhhhhhhh.....hhhhhhhhhhhh..eeeeeeeeee...hhhhhhhhh.....hhhhhhhhhhhhhhh...eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p7h A  21 YNFDFDVmHPFmVRAFTPFFRPGNLLELGSFKGDFTSRLQEHFNDITCVEASEEAISHAQGRLKDGITYIHSRFEDAQLPRRYDNIVLTHVLEHIDDPVALLKRINDDWLAEGGRLFLVCPNANAVSRQIAVKmGIISHNSAVTEAEFAHGHRCTYALDTLERDASRAGLQVTYRSGIFFKALANFQWDQILQTDILSKEYLDGCYQLGQQYPDLCASIFLLCEKGINQ 249
                                   |30 |      40        50        60        70        80        90       100       110       120       130       140       150   |   160       170       180       190       200       210       220       230       240         
                                  28-MSE                                                                                                                       154-MSE                                                                                           
                                      32-MSE                                                                                                                                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:226
 aligned with Q6D6E7_PECAS | Q6D6E7 from UniProtKB/TrEMBL  Length:249

    Alignment length:226
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
         Q6D6E7_PECAS    21 YNFDFDVMHPFMVRAFTPFFRPGNLLELGSFKGDFTSRLQEHFNDITCVEASEEAISHAQGRLKDGITYIHSRFEDAQLPRRYDNIVLTHVLEHIDDPVALLKRINDDWLAEGGRLFLVCPNANAVSRQIAVKMGIISHNSAVTEAEFAHGHRCTYALDTLERDASRAGLQVTYRSGIFFKALANFQWDQILQTDILSKEYLDGCYQLGQQYPDLCASIFLLCEKG 246
               SCOP domains d2p7hb_ B: Hypothetical protein ECA1738                                                                                                                                                                                            SCOP domains
               CATH domains 2p7hB00 B:21-246 Vaccinia Virus protein VP39                                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhh.....eeeee.hhhhhhhhhh.....eeeee.hhhhh.....eeeeeee.hhhhh.hhhhhhhhhhhh.eeeeeeeeeeee...hhhhhhhhhh.........hhhhhhh......hhhhhhhhhhhh..eeeeeeeeee...hhhhhhhhhh....hhhhhhhhhhhhhhh...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p7h B  21 YNFDFDVmHPFmVRAFTPFFRPGNLLELGSFKGDFTSRLQEHFNDITCVEASEEAISHAQGRLKDGITYIHSRFEDAQLPRRYDNIVLTHVLEHIDDPVALLKRINDDWLAEGGRLFLVCPNANAVSRQIAVKmGIISHNSAVTEAEFAHGHRCTYALDTLERDASRAGLQVTYRSGIFFKALANFQWDQILQTDILSKEYLDGCYQLGQQYPDLCASIFLLCEKG 246
                                   |30 |      40        50        60        70        80        90       100       110       120       130       140       150   |   160       170       180       190       200       210       220       230       240      
                                  28-MSE                                                                                                                       154-MSE                                                                                        
                                      32-MSE                                                                                                                                                                                                                  

Chain C from PDB  Type:PROTEIN  Length:229
 aligned with Q6D6E7_PECAS | Q6D6E7 from UniProtKB/TrEMBL  Length:249

    Alignment length:229
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
         Q6D6E7_PECAS    21 YNFDFDVMHPFMVRAFTPFFRPGNLLELGSFKGDFTSRLQEHFNDITCVEASEEAISHAQGRLKDGITYIHSRFEDAQLPRRYDNIVLTHVLEHIDDPVALLKRINDDWLAEGGRLFLVCPNANAVSRQIAVKMGIISHNSAVTEAEFAHGHRCTYALDTLERDASRAGLQVTYRSGIFFKALANFQWDQILQTDILSKEYLDGCYQLGQQYPDLCASIFLLCEKGINQ 249
               SCOP domains d2p7hc_ C: Hypothetical protein ECA1738                                                                                                                                                                                               SCOP domains
               CATH domains 2p7hC00 C:21-249 Vaccinia Virus protein VP39                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhh.....eeeee.hhhhhhhhhh.....eeeee.hhhhh.....eeeeeee.hhhhh.hhhhhhhhhhhhheeeeeeeeeeee...hhhhhhhhhh.........hhhhhhhh.....hhhhhhhhhhhh..eeeeeeeeee...hhhhhhhhhh....hhhhhhhhhhhhhhhhh.eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p7h C  21 YNFDFDVmHPFmVRAFTPFFRPGNLLELGSFKGDFTSRLQEHFNDITCVEASEEAISHAQGRLKDGITYIHSRFEDAQLPRRYDNIVLTHVLEHIDDPVALLKRINDDWLAEGGRLFLVCPNANAVSRQIAVKmGIISHNSAVTEAEFAHGHRCTYALDTLERDASRAGLQVTYRSGIFFKALANFQWDQILQTDILSKEYLDGCYQLGQQYPDLCASIFLLCEKGINQ 249
                                   |30 |      40        50        60        70        80        90       100       110       120       130       140       150   |   160       170       180       190       200       210       220       230       240         
                                  28-MSE                                                                                                                       154-MSE                                                                                           
                                      32-MSE                                                                                                                                                                                                                     

Chain D from PDB  Type:PROTEIN  Length:226
 aligned with Q6D6E7_PECAS | Q6D6E7 from UniProtKB/TrEMBL  Length:249

    Alignment length:226
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
         Q6D6E7_PECAS    21 YNFDFDVMHPFMVRAFTPFFRPGNLLELGSFKGDFTSRLQEHFNDITCVEASEEAISHAQGRLKDGITYIHSRFEDAQLPRRYDNIVLTHVLEHIDDPVALLKRINDDWLAEGGRLFLVCPNANAVSRQIAVKMGIISHNSAVTEAEFAHGHRCTYALDTLERDASRAGLQVTYRSGIFFKALANFQWDQILQTDILSKEYLDGCYQLGQQYPDLCASIFLLCEKG 246
               SCOP domains d2p7hd_ D: Hypothetical protein ECA1738                                                                                                                                                                                            SCOP domains
               CATH domains 2p7hD00 D:21-246 Vaccinia Virus protein VP39                                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhh.....eeeee.hhhhhhhhhhhh...eeeee.hhhhh.....eeeeeee.hhhhh.hhhhhhhhhhhh.eeeeeeeeeeee...hhhhhhhhhh.........hhhhhhh......hhhhhhhhhhhh..eeeeeeeeee...hhhhhhhhhh....hhhhhhhhhhhhhhhhh.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p7h D  21 YNFDFDVmHPFmVRAFTPFFRPGNLLELGSFKGDFTSRLQEHFNDITCVEASEEAISHAQGRLKDGITYIHSRFEDAQLPRRYDNIVLTHVLEHIDDPVALLKRINDDWLAEGGRLFLVCPNANAVSRQIAVKmGIISHNSAVTEAEFAHGHRCTYALDTLERDASRAGLQVTYRSGIFFKALANFQWDQILQTDILSKEYLDGCYQLGQQYPDLCASIFLLCEKG 246
                                   |30 |      40        50        60        70        80        90       100       110       120       130       140       150   |   160       170       180       190       200       210       220       230       240      
                                  28-MSE                                                                                                                       154-MSE                                                                                        
                                      32-MSE                                                                                                                                                                                                                  

   Legend:   → Mismatch (orange background)
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    → 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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2P7H)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2P7H)

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