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(-) Description

Title :  CRYSTAL STRUCTURE OF A PROTEIN MEMBER OF THE UPF0052 FAMILY (BH3568) FROM BACILLUS HALODURANS AT 2.60 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  30 Nov 06  (Deposition) - 19 Dec 06  (Release) - 23 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Nad-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Hypothetical Protein (Np_244435. 1) Fro Bacillus Halodurans At 2. 60 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_244435.1
    Organism Scientific: BACILLUS HALODURANS
    Organism Taxid: 86665

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 34)

Asymmetric Unit (3, 34)
No.NameCountTypeFull Name
1MSE22Mod. Amino AcidSELENOMETHIONINE
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3SO48Ligand/IonSULFATE ION
Biological Unit 1 (3, 17)
No.NameCountTypeFull Name
1MSE11Mod. Amino AcidSELENOMETHIONINE
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3SO44Ligand/IonSULFATE ION
Biological Unit 2 (3, 17)
No.NameCountTypeFull Name
1MSE11Mod. Amino AcidSELENOMETHIONINE
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3SO44Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER B:41 , SER B:42 , ARG B:58 , ARG B:78 , ASN B:92BINDING SITE FOR RESIDUE SO4 B 323
02AC2SOFTWAREGLY A:40 , SER A:41 , SER A:42 , ARG A:58 , ARG A:78 , ASN A:92BINDING SITE FOR RESIDUE SO4 A 323
03AC3SOFTWARESER D:41 , SER D:42 , ARG D:58 , ARG D:78 , ASN D:92 , HOH D:438 , HOH D:469BINDING SITE FOR RESIDUE SO4 D 323
04AC4SOFTWARESER C:41 , SER C:42 , ARG C:58 , ARG C:78 , ASN C:92 , HOH C:463BINDING SITE FOR RESIDUE SO4 C 323
05AC5SOFTWAREGLY A:11 , GLY A:12 , THR A:13 , GLY A:14 , GLY A:186 , SER A:187 , SER A:191 , NAD A:400 , HOH A:448BINDING SITE FOR RESIDUE SO4 A 324
06AC6SOFTWAREGLY C:11 , GLY C:12 , THR C:13 , GLY C:14 , GLY C:186 , SER C:187 , SER C:191 , NAD C:400 , HOH C:406BINDING SITE FOR RESIDUE SO4 C 324
07AC7SOFTWAREGLY D:11 , GLY D:12 , THR D:13 , GLY D:186 , SER D:187 , SER D:191 , NAD D:400 , HOH D:403 , HOH D:467BINDING SITE FOR RESIDUE SO4 D 324
08AC8SOFTWAREGLY B:11 , GLY B:12 , THR B:13 , GLY B:186 , SER B:187 , SER B:191 , NAD B:400 , HOH B:406 , HOH B:465BINDING SITE FOR RESIDUE SO4 B 324
09AC9SOFTWARETHR A:13 , GLY A:14 , GLY A:186 , SER A:187 , ASN A:217 , VAL A:218 , MSE A:219 , GLN A:221 , LYS A:263 , TYR A:264 , GLU A:267 , VAL A:298 , ARG A:300 , HIS A:301 , SO4 A:324 , HOH A:418BINDING SITE FOR RESIDUE NAD A 400
10BC1SOFTWARETHR B:13 , GLY B:14 , GLY B:186 , SER B:187 , ASN B:217 , VAL B:218 , MSE B:219 , GLN B:221 , LYS B:263 , TYR B:264 , GLU B:267 , VAL B:298 , ARG B:300 , HIS B:301 , SO4 B:324 , HOH B:424 , HOH B:456BINDING SITE FOR RESIDUE NAD B 400
11BC2SOFTWARETHR C:13 , GLY C:14 , GLY C:186 , SER C:187 , ASN C:217 , VAL C:218 , MSE C:219 , GLN C:221 , LYS C:263 , TYR C:264 , GLU C:267 , VAL C:298 , ARG C:300 , HIS C:301 , SO4 C:324 , HOH C:417 , HOH C:438BINDING SITE FOR RESIDUE NAD C 400
12BC3SOFTWARETHR D:13 , GLY D:14 , GLY D:186 , SER D:187 , ASN D:217 , VAL D:218 , MSE D:219 , GLN D:221 , LYS D:263 , TYR D:264 , GLU D:267 , VAL D:298 , ARG D:300 , HIS D:301 , SO4 D:324 , HOH D:431 , HOH D:474BINDING SITE FOR RESIDUE NAD D 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O2Z)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Thr A:161 -Pro A:162
2Gly A:184 -Pro A:185
3Thr B:161 -Pro B:162
4Gly B:184 -Pro B:185
5Thr C:161 -Pro C:162
6Gly C:184 -Pro C:185
7Thr D:161 -Pro D:162
8Gly D:184 -Pro D:185

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O2Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O2Z)

(-) Exons   (0, 0)

(no "Exon" information available for 2O2Z)

(-) 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:310
 aligned with GNGF_BACHD | Q9K706 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:313
                             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       279       289       299       309   
           GNGF_BACHD     - -MKKKNVVVFGGGTGLSVLLRGLKTFPVSITAIVTVADDGGSSGRLRKELDIPPPGDVRNVLVALSEVEPLLEQLFQHRFENGNGLSGHSLGNLLLAGMTSITGDFARGISEMSKVLNVRGKVLPASNRSIILHGEMEDGTIVTGESSIPKAGKKIKRVFLTPKDTKPLREGLEAIRKADVIVIGPGSLYTSVLPNLLVPGICEAIKQSTARKVYICNVMTQNGETDGYTASDHLQAIMDHCGVGIVDDILVHGEPISDTVKAKYAKEKAEPVIVDEHKLKALGVGTISDYFVLEQDDVLRHNASKVSEAILE 312
               SCOP domains d2o2za_ A: automated matches                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.hhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhh.....-.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee......eeeeee....eee...hhhhhh..eeeeeee......hhhhhhhhhhh.eeee.......hhhhhhh..hhhhhhhhh..eeeee.............hhhhhhhhhhhhhh.....eeeee....hhhhhhhhhh........hhhhhhhh..eeeee..ee..--..eehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o2z A   0 GmKKKNVIVFGGGTGLSVLLRGLKTFPVSITAIVTVADDGGSSGRLRKELDIPPPGDVRNVLVALSEVEPLLEQLFQHRFENG-GLSGHSLGNLLLAGmTSITGDFARGISEmSKVLNVRGKVLPASNRSIILHGEmEDGTIVTGESSIPKAGKKIKRVFLTPKDTKPLREGLEAIRKADVIVIGPGSLYTSVLPNLLVPGICEAIKQSTARKVYICNVmTQNGETDGYTASDHLQAImDHCGVGIVDDILVHGEPISDTVKAKYAKEKAEPVIVDEHKLKALGVGTISDYFVLEQ--VLRHNASKVSEAILE 312
                             |       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       279       289     | 299       309   
                             |                                                                               82 |            98-MSE       112-MSE                 136-MSE                                                                            219-MSE            238-MSE                                                  295  |              
                             1-MSE                                                                             84                                                                                                                                                                                                                   298              


Chain B from PDB  Type:PROTEIN  Length:308
 aligned with GNGF_BACHD | Q9K706 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:310
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312
           GNGF_BACHD     3 KKNVVVFGGGTGLSVLLRGLKTFPVSITAIVTVADDGGSSGRLRKELDIPPPGDVRNVLVALSEVEPLLEQLFQHRFENGNGLSGHSLGNLLLAGMTSITGDFARGISEMSKVLNVRGKVLPASNRSIILHGEMEDGTIVTGESSIPKAGKKIKRVFLTPKDTKPLREGLEAIRKADVIVIGPGSLYTSVLPNLLVPGICEAIKQSTARKVYICNVMTQNGETDGYTASDHLQAIMDHCGVGIVDDILVHGEPISDTVKAKYAKEKAEPVIVDEHKLKALGVGTISDYFVLEQDDVLRHNASKVSEAILE 312
               SCOP domains d2o2zb_ B: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhh.....-.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee......eeeeee....eee...hhhhhh..eeeeeee......hhhhhhhhhh..eeee.......hhhhhhh..hhhhhhhhh..eeeee.............hhhhhhhhhhhhhh.....eeeee....hhhhhhhhhh........hhhhhhhh..eeeee..ee.-....eehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o2z B   3 KKNVIVFGGGTGLSVLLRGLKTFPVSITAIVTVADDGGSSGRLRKELDIPPPGDVRNVLVALSEVEPLLEQLFQHRFENG-GLSGHSLGNLLLAGmTSITGDFARGISEmSKVLNVRGKVLPASNRSIILHGEmEDGTIVTGESSIPKAGKKIKRVFLTPKDTKPLREGLEAIRKADVIVIGPGSLYTSVLPNLLVPGICEAIKQSTARKVYICNVmTQNGETDGYTASDHLQAImDHCGVGIVDDILVHGEPISDTVKAKYAKEKAEPVIVDEHKLKALGVGTISDYFVLE-DDVLRHNASKVSEAILE 312
                                    12        22        32        42        52        62        72        82 |      92     | 102       112       122       132   |   142       152       162       172       182       192       202       212      |222       232     | 242       252       262       272       282       292 | |   302       312
                                                                                                          82 |            98-MSE       112-MSE                 136-MSE                                                                            219-MSE            238-MSE                                                 294 |                
                                                                                                            84                                                                                                                                                                                                                 296                


Chain C from PDB  Type:PROTEIN  Length:309
 aligned with GNGF_BACHD | Q9K706 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:310
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312
           GNGF_BACHD     3 KKNVVVFGGGTGLSVLLRGLKTFPVSITAIVTVADDGGSSGRLRKELDIPPPGDVRNVLVALSEVEPLLEQLFQHRFENGNGLSGHSLGNLLLAGMTSITGDFARGISEMSKVLNVRGKVLPASNRSIILHGEMEDGTIVTGESSIPKAGKKIKRVFLTPKDTKPLREGLEAIRKADVIVIGPGSLYTSVLPNLLVPGICEAIKQSTARKVYICNVMTQNGETDGYTASDHLQAIMDHCGVGIVDDILVHGEPISDTVKAKYAKEKAEPVIVDEHKLKALGVGTISDYFVLEQDDVLRHNASKVSEAILE 312
               SCOP domains d2o2zc_ C: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhh.....-.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee......eeeeee....eee...hhhhhh..eeeeeee......hhhhhhhhhhh.eeee.......hhhhhhh..hhhhhhhhh..eeeee.............hhhhhhhhhhhhhh.....eeeee....hhhhhhhhhh........hhhhhhhh..eeeee..eee....eeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o2z C   3 KKNVIVFGGGTGLSVLLRGLKTFPVSITAIVTVADDGGSSGRLRKELDIPPPGDVRNVLVALSEVEPLLEQLFQHRFENG-GLSGHSLGNLLLAGmTSITGDFARGISEmSKVLNVRGKVLPASNRSIILHGEmEDGTIVTGESSIPKAGKKIKRVFLTPKDTKPLREGLEAIRKADVIVIGPGSLYTSVLPNLLVPGICEAIKQSTARKVYICNVmTQNGETDGYTASDHLQAImDHCGVGIVDDILVHGEPISDTVKAKYAKEKAEPVIVDEHKLKALGVGTISDYFVLEQDDVLRHNASKVSEAILE 312
                                    12        22        32        42        52        62        72        82 |      92     | 102       112       122       132   |   142       152       162       172       182       192       202       212      |222       232     | 242       252       262       272       282       292       302       312
                                                                                                          82 |            98-MSE       112-MSE                 136-MSE                                                                            219-MSE            238-MSE                                                                      
                                                                                                            84                                                                                                                                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:310
 aligned with GNGF_BACHD | Q9K706 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:312
                                    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       280       290       300       310  
           GNGF_BACHD     1 MKKKNVVVFGGGTGLSVLLRGLKTFPVSITAIVTVADDGGSSGRLRKELDIPPPGDVRNVLVALSEVEPLLEQLFQHRFENGNGLSGHSLGNLLLAGMTSITGDFARGISEMSKVLNVRGKVLPASNRSIILHGEMEDGTIVTGESSIPKAGKKIKRVFLTPKDTKPLREGLEAIRKADVIVIGPGSLYTSVLPNLLVPGICEAIKQSTARKVYICNVMTQNGETDGYTASDHLQAIMDHCGVGIVDDILVHGEPISDTVKAKYAKEKAEPVIVDEHKLKALGVGTISDYFVLEQDDVLRHNASKVSEAILE 312
               SCOP domains d2o2zd_ D: automated matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhh.....-.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee......eeeeee....eee...hhhhhh..eeeeeee......hhhhhhhhhhh.eeee........hhhhhh..hhhhhhhhh..eeeee.............hhhhhhhhhhhhhh.....eeeee....hhhhhhhhhh........hhhhhhhh..eeeee..eee.-..eeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2o2z D   1 mKKKNVIVFGGGTGLSVLLRGLKTFPVSITAIVTVADDGGSSGRLRKELDIPPPGDVRNVLVALSEVEPLLEQLFQHRFENG-GLSGHSLGNLLLAGmTSITGDFARGISEmSKVLNVRGKVLPASNRSIILHGEmEDGTIVTGESSIPKAGKKIKRVFLTPKDTKPLREGLEAIRKADVIVIGPGSLYTSVLPNLLVPGICEAIKQSTARKVYICNVmTQNGETDGYTASDHLQAImDHCGVGIVDDILVHGEPISDTVKAKYAKEKAEPVIVDEHKLKALGVGTISDYFVLEQ-DVLRHNASKVSEAILE 312
                            |       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       280       290    | |300       310  
                            1-MSE                                                                           82 |            98-MSE       112-MSE                 136-MSE                                                                            219-MSE            238-MSE                                                  295 |               
                                                                                                              84                                                                                                                                                                                                                  297
   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2O2Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2O2Z)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (GNGF_BACHD | Q9K706)
biological process
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  2o2z
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  GNGF_BACHD | Q9K706
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GNGF_BACHD | Q9K706: 2hzb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2O2Z)