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(-) Description

Title :  CRYSTAL STRUCTURE OF A HD-DOMAIN PHOSPHOHYDROLASE (LIN2634) FROM LISTERIA INNOCUA AT 1.98 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  12 May 10  (Deposition) - 26 May 10  (Release) - 26 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  B,C  (1x)
Keywords :  Hd-Domain Phosphohydrolase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Hd-Domain Phosphohydrolase (Lin2634) From Listeria Innocua At 1. 98 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LIN2634 PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LIN2634
    Organism Scientific: LISTERIA INNOCUA
    Organism Taxid: 1642

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC
Biological Unit 2 (2x): A  
Biological Unit 3 (1x):  BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 28)

Asymmetric Unit (3, 28)
No.NameCountTypeFull Name
1CA11Ligand/IonCALCIUM ION
2MSE15Mod. Amino AcidSELENOMETHIONINE
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 34)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE30Mod. Amino AcidSELENOMETHIONINE
3PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE10Mod. Amino AcidSELENOMETHIONINE
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 3 (2, 11)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE10Mod. Amino AcidSELENOMETHIONINE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:18 , HIS A:33 , HIS A:67 , ASP A:68 , LYS A:78 , ASP A:137 , HOH A:580BINDING SITE FOR RESIDUE CA A 301
02AC2SOFTWARETYR A:17 , HOH A:409 , HOH A:446BINDING SITE FOR RESIDUE CA A 304
03AC3SOFTWAREHIS A:67 , ASP A:68 , HOH A:522 , HOH A:527 , HOH A:583 , HOH A:655BINDING SITE FOR RESIDUE CA A 305
04AC4SOFTWAREASP A:50 , HOH A:605 , GLU B:54 , HOH B:457 , HOH B:518BINDING SITE FOR RESIDUE CA A 306
05AC5SOFTWAREHOH A:366 , HOH A:516 , ASP B:50 , HOH B:377 , HOH C:389 , HOH C:560BINDING SITE FOR RESIDUE CA A 307
06AC6SOFTWAREGLU A:184 , HOH A:378 , HOH A:512 , HOH A:586 , HOH A:632 , HOH A:675BINDING SITE FOR RESIDUE CA A 308
07AC7SOFTWAREGLY A:75 , GLY B:75BINDING SITE FOR RESIDUE PEG A 313
08AC8SOFTWAREHIS B:33 , HIS B:67 , ASP B:68 , ASP B:137 , HOH B:576BINDING SITE FOR RESIDUE CA B 302
09AC9SOFTWAREHOH B:472 , HOH B:476 , HOH B:592 , HOH B:628BINDING SITE FOR RESIDUE CA B 309
10BC1SOFTWAREHIS B:67 , ASP B:68 , HOH B:477 , HOH B:550 , HOH B:575 , HOH B:576 , HOH B:686BINDING SITE FOR RESIDUE CA B 310
11BC2SOFTWARELYS B:131 , HOH B:646 , HOH B:656 , HOH B:667BINDING SITE FOR RESIDUE PEG B 312
12BC3SOFTWAREARG C:18 , HIS C:33 , HIS C:67 , ASP C:68 , ASP C:137BINDING SITE FOR RESIDUE CA C 303
13BC4SOFTWAREHIS C:67 , ASP C:68 , SER C:70 , GLU C:96 , HOH C:336BINDING SITE FOR RESIDUE CA C 311

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MZO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MZO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MZO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MZO)

(-) Exons   (0, 0)

(no "Exon" information available for 3MZO)

(-) 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:210
 aligned with Q928A2_LISIN | Q928A2 from UniProtKB/TrEMBL  Length:215

    Alignment length:210
                             1                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209
         Q928A2_LISIN     - -MGIHQYFQSLSDLENIYRCPGKFKYQEHSVAEHSYKVTSIAQFFGAVEEDAGNEVNWRALYEKALNHDYSELFIGDIKTPVKYATTELREMLSEVEESMTKNFISREIPATFQPIYRHLLKEGKDSTLEGKILAISDKVDLLYESFGEIQKGNPENIFVEIYSEALATIYEYREMASVKYFLKEILPDMLAEKGIEKTELPQLTTEITT 209
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mzo A   0 GmGIHQYFQSLSDLENIYRCPGKFKYQEHSVAEHSYKVTSIAQFFGAVEEDAGNEVNWRALYEKALNHDYSELFIGDIKTPVKYATTELREmLSEVEESmTKNFISREIPATFQPIYRHLLKEGKDSTLEGKILAISDKVDLLYESFGEIQKGNPENIFVEIYSEALATIYEYREmASVKYFLKEILPDmLAEKGIEKTELPQLTTEITT 209
                             |       9        19        29        39        49        59        69        79        89 |      99       109       119       129       139       149       159       169     | 179       189       199       209
                             |                                                                                        91-MSE  99-MSE                                                                     175-MSE       189-MSE                
                             1-MSE                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:211
 aligned with Q928A2_LISIN | Q928A2 from UniProtKB/TrEMBL  Length:215

    Alignment length:211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
         Q928A2_LISIN     1 MGIHQYFQSLSDLENIYRCPGKFKYQEHSVAEHSYKVTSIAQFFGAVEEDAGNEVNWRALYEKALNHDYSELFIGDIKTPVKYATTELREMLSEVEESMTKNFISREIPATFQPIYRHLLKEGKDSTLEGKILAISDKVDLLYESFGEIQKGNPENIFVEIYSEALATIYEYREMASVKYFLKEILPDMLAEKGIEKTELPQLTTEITTKA 211
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mzo B   1 mGIHQYFQSLSDLENIYRCPGKFKYQEHSVAEHSYKVTSIAQFFGAVEEDAGNEVNWRALYEKALNHDYSELFIGDIKTPVKYATTELREmLSEVEESmTKNFISREIPATFQPIYRHLLKEGKDSTLEGKILAISDKVDLLYESFGEIQKGNPENIFVEIYSEALATIYEYREmASVKYFLKEILPDmLAEKGIEKTELPQLTTEITTKA 211
                            |       10        20        30        40        50        60        70        80        90|      100       110       120       130       140       150       160       170    |  180       190       200       210 
                            1-MSE                                                                                    91-MSE  99-MSE                                                                     175-MSE       189-MSE                  


Chain C from PDB  Type:PROTEIN  Length:196
 aligned with Q928A2_LISIN | Q928A2 from UniProtKB/TrEMBL  Length:215

    Alignment length:211
                             1                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209 
         Q928A2_LISIN     - -MGIHQYFQSLSDLENIYRCPGKFKYQEHSVAEHSYKVTSIAQFFGAVEEDAGNEVNWRALYEKALNHDYSELFIGDIKTPVKYATTELREMLSEVEESMTKNFISREIPATFQPIYRHLLKEGKDSTLEGKILAISDKVDLLYESFGEIQKGNPENIFVEIYSEALATIYEYREMASVKYFLKEILPDMLAEKGIEKTELPQLTTEITTK 210
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -HD_2-3mzoC01 C:1-210                                                                                                                                                                                               Pfam domains (1)
           Pfam domains (2) -HD_2-3mzoC02 C:1-210                                                                                                                                                                                               Pfam domains (2)
           Pfam domains (3) -HD_2-3mzoC03 C:1-210                                                                                                                                                                                               Pfam domains (3)
         Sec.struct. author ..hhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.---------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mzo C   0 GmGIHQYFQSLSDLENIYRCPGKFKYQEHSVAEHSYKVTSIAQFFGAVEEDAGNEVNWRALYEKALNHDYSELFI---------------EmLSEVEESmTKNFISREIPATFQPIYRHLLKEGKDSTLEGKILAISDKVDLLYESFGEIQKGNPENIFVEIYSEALATIYEYREmASVKYFLKEILPDmLAEKGIEKTELPQLTTEITTK 210
                             |       9        19        29        39        49        59        69    |    -         -||      99       109       119       129       139       149       159       169     | 179       189       199       209 
                             1-MSE                                                                   74              90|      99-MSE                                                                     175-MSE       189-MSE                 
                                                                                                                      91-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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3MZO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MZO)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: HD_PDEase (93)
(-)
Family: HD_2 (1)
(-)
Listeria innocua (1)
1aHD_2-3mzoC01C:1-210
1bHD_2-3mzoC02C:1-210
1cHD_2-3mzoC03C:1-210

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q928A2_LISIN | Q928A2)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  3mzo
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