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(-) Description

Title :  CRYSTAL STRUCTURE MOLYBDENUM STORAGE PROTEIN WITH FULLY MO-LOADED CAVITY
 
Authors :  J. Poppe, E. Warkentin, U. Demmer, U. Ermler
Date :  27 Oct 13  (Deposition) - 13 Aug 14  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Rossmann Fold, Molybdenum Storage, Atp Binding, Molybdenum Binding, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Poppe, E. Warkentin, U. Demmer, B. Kowalewski, T. Dierks, K. Schneider, U. Ermler
Structural Diversity Of Polyoxomolybdate Clusters Along The Three-Fold Axis Of The Molybdenum Storage Protein.
J. Inorg. Biochem. V. 138 122 2014
PubMed-ID: 24945101  |  Reference-DOI: 10.1016/J.JINORGBIO.2014.05.009

(-) Compounds

Molecule 1 - MOLYBDENUM STORAGE PROTEIN SUBUNIT BETA
    Chains: B
    Organism Scientific: AZOTOBACTER VINELANDII
    Organism Taxid: 322710
    Strain: ATCC 13705
 
Molecule 2 - MOLYBDENUM STORAGE PROTEIN SUBUNIT ALPHA
    Chains: A
    Organism Scientific: AZOTOBACTER VINELANDII
    Organism Taxid: 322710
    Strain: ATCC 13705

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 27)

Asymmetric Unit (6, 27)
No.NameCountTypeFull Name
18M02Ligand/IonBIS(MU4-OXO)-TETRAKIS(MU3-OXO)-HEXAKIS(MU2-OXO)-HEXADECAOXO-OCTAMOLYBDENUM (VI)
2ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3M101Ligand/Ion(MU3-OXO)-TRIS(MU2-OXO)-NONAKISOXO-TRIMOLYBDENUM (VI)
4MG1Ligand/IonMAGNESIUM ION
5MO20Ligand/IonMOLYBDENUM ATOM
6PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (4, 18)
No.NameCountTypeFull Name
18M06Ligand/IonBIS(MU4-OXO)-TETRAKIS(MU3-OXO)-HEXAKIS(MU2-OXO)-HEXADECAOXO-OCTAMOLYBDENUM (VI)
2ATP6Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3M103Ligand/Ion(MU3-OXO)-TRIS(MU2-OXO)-NONAKISOXO-TRIMOLYBDENUM (VI)
4MG-1Ligand/IonMAGNESIUM ION
5MO-1Ligand/IonMOLYBDENUM ATOM
6PO43Ligand/IonPHOSPHATE ION

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS B:42 , GLY B:44 , GLY B:45 , GLN B:46 , SER B:47 , GLY B:77 , ALA B:78 , GLY B:79 , THR B:169 , LYS B:189 , ASP B:190 , GLY B:193 , TYR B:195 , ALA B:197 , ASN B:198 , PRO B:199 , LYS B:200 , SER B:224 , ILE B:225 , HOH B:402 , HOH B:496 , HOH B:564BINDING SITE FOR RESIDUE ATP B 301
02AC2SOFTWAREARG B:210 , GLU B:242 , HIS B:262BINDING SITE FOR RESIDUE PO4 B 302
03AC3SOFTWARETYR A:155 , HIS A:156 , HIS A:157 , HIS A:158 , 8M0 A:303 , HOH A:463 , GLY B:127 , GLY B:128 , ALA B:129 , GLY B:130 , PHE B:146 , SER B:147 , MET B:149 , PRO B:150 , PRO B:151 , LEU B:176 , PHE B:180 , MO B:309 , MO B:318 , HOH B:417 , HOH B:450 , HOH B:490 , HOH B:534 , HOH B:541BINDING SITE FOR RESIDUE 8M0 B 303
04AC4SOFTWAREMO B:305 , MO B:308 , MO B:309BINDING SITE FOR RESIDUE MO B 304
05AC5SOFTWAREMO B:304 , MO B:306 , MO B:309BINDING SITE FOR RESIDUE MO B 305
06AC6SOFTWAREMO B:305 , MO B:307 , MO B:309BINDING SITE FOR RESIDUE MO B 306
07AC7SOFTWAREMO B:306 , MO B:308 , MO B:309BINDING SITE FOR RESIDUE MO B 307
08AC8SOFTWAREMO B:304 , MO B:307 , MO B:309BINDING SITE FOR RESIDUE MO B 308
09AC9SOFTWARE8M0 B:303 , MO B:304 , MO B:305 , MO B:306 , MO B:307 , MO B:308BINDING SITE FOR RESIDUE MO B 309
10BC1SOFTWAREMO B:311 , MO B:312BINDING SITE FOR RESIDUE MO B 310
11BC2SOFTWAREMO B:310BINDING SITE FOR RESIDUE MO B 311
12BC3SOFTWAREMO B:310 , MO B:313 , MO B:314BINDING SITE FOR RESIDUE MO B 312
13BC4SOFTWAREMO B:312 , MO B:314 , HOH B:445BINDING SITE FOR RESIDUE MO B 313
14BC5SOFTWAREMO B:312 , MO B:313BINDING SITE FOR RESIDUE MO B 314
15BC6SOFTWAREMO B:316 , MO B:318 , MO B:319BINDING SITE FOR RESIDUE MO B 315
16BC7SOFTWAREMO B:315 , MO B:317 , MO B:318BINDING SITE FOR RESIDUE MO B 316
17BC8SOFTWAREMO B:316 , MO B:318 , MO B:319BINDING SITE FOR RESIDUE MO B 317
18BC9SOFTWARE8M0 B:303 , MO B:315 , MO B:316 , MO B:317 , MO B:319BINDING SITE FOR RESIDUE MO B 318
19CC1SOFTWAREMO B:315 , MO B:317 , MO B:318BINDING SITE FOR RESIDUE MO B 319
20CC2SOFTWARELYS A:45 , GLY A:47 , GLY A:48 , ARG A:49 , GLY A:79 , ALA A:80 , GLY A:81 , ARG A:85 , GLU A:190 , ASN A:191 , VAL A:192 , GLY A:194 , ILE A:195 , TYR A:196 , ASP A:199 , PRO A:200 , ASN A:201 , PRO A:225 , LEU A:226 , PRO A:227 , MG A:302 , HOH A:423 , HOH A:429 , HOH A:437 , HOH A:438 , HOH A:439 , HOH A:441 , HOH A:450 , HOH A:479 , HOH A:481 , HOH B:414BINDING SITE FOR RESIDUE ATP A 301
21CC3SOFTWAREGLU A:190 , PRO A:227 , ATP A:301 , HOH A:437 , HOH A:439BINDING SITE FOR RESIDUE MG A 302
22CC4SOFTWAREPRO A:103 , ALA A:106 , SER A:107 , GLY A:110 , GLN A:111 , HIS A:114 , TYR A:127 , GLU A:129 , HIS A:130 , PRO A:131 , SER A:150 , PRO A:153 , PRO A:154 , HIS A:156 , HOH A:487 , HOH A:509 , HOH A:536 , HOH A:587 , 8M0 B:303BINDING SITE FOR RESIDUE 8M0 A 303
23CC5SOFTWARETHR A:132 , GLN A:136 , ILE A:139 , HIS A:140 , HOH A:457 , HOH A:585BINDING SITE FOR RESIDUE M10 A 304
24CC6SOFTWAREMO A:306 , MO A:307 , MO A:308 , HOH A:401 , HOH A:405 , HOH A:406 , HOH A:407BINDING SITE FOR RESIDUE MO A 305
25CC7SOFTWAREMO A:305 , MO A:307 , MO A:308 , HOH A:401 , HOH A:404 , HOH A:407BINDING SITE FOR RESIDUE MO A 306
26CC8SOFTWAREMO A:305 , MO A:306 , MO A:308 , HOH A:401 , HOH A:402 , HOH A:403 , HOH A:404 , HOH A:407BINDING SITE FOR RESIDUE MO A 307
27CC9SOFTWAREMO A:305 , MO A:306 , MO A:307 , HOH A:401 , HOH A:585BINDING SITE FOR RESIDUE MO A 308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NDR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NDR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NDR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NDR)

(-) Exons   (0, 0)

(no "Exon" information available for 4NDR)

(-) 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:245
                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeehhhhhh.hhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.hhhhhhhhhhhhhhhh.eeeee....hhhhh.........hhhhhhhhhhhhhh..eeeeee....ee.............ee.eeehhhhhh.......hhhhhhhhhh.....eeeeee....hhhhhhhh.....eeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ndr A  32 KRPIRLLPWLQVVKIGGRVMDRGADAILPLVEELRKLLPEHRLLILTGAGVRARHVFSVGLDLGLPVGSLAPLAASEAGQNGHILAAMLASEGVSYVEHPTVADQLAIHLSATRAVVGSAFPPYHHHEFPGSRIPPHRADTGAFLLADAFGAAGLTIVENVDGIYTADPNGPDRGQARFLPETSATDLAKSEGPLPVDRALLDVMATARHIERVQVVNGLVPGRLTAALRGEHVGTLIRTGVRPA 276
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271     


Chain B from PDB  Type:PROTEIN  Length:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...hhhhhhhhhh.........eeeeee....hhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh....eeeee....hhhhh...........hhhhhhhhhhhhhh..eeeeee....ee...........ee.eeehhhhhhh.......hhhhhhhhhhh....eeeeee....hhhhhhhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ndr B   3 NSTAELEELLMQRSLTDPQLQAAAAAAADFRILPDATVIKIGGQSVIDRGRAAVYPLVDEIVAARKNHKLLIGTGAGTRARHLYSIAAGLGLPAGVLAQLGSSVADQNAAMLGQLLAKHGIPVVGGAGLSAVPLSLAEVNAVVFSGMPPYKLWMRPAAEGVIPPYRTDAGCFLLAEQFGCKQMIFVKDEDGLYTANPKTSKDATFIPRISVDEMKAKGLHDSILEFPVLDLLQSAQHVREVQVVNGLVPGNLTRALAGEHVGTIITAS 270
                                    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
   Legend:   → Mismatch (orange background)
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4NDR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NDR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NDR)

(-) Gene Ontology  (4, 8)

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 Related Entries

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

UniProtKB/Swiss-Prot
        MOSA_AZOVD | P84308: 2ogx 4f6t 4ndo 4ndp 4ndq
        MOSB_AZOVD | P84253: 2ogx 4f6t 4ndo 4ndp 4ndq

(-) Related Entries Specified in the PDB File

2ogx 4f6t 4ndo 4ndp 4ndq 4ndr