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(-) Description

Title :  UNACTIVATED RUBISCO WITH MAGNESIUM AND A WATER MOLECULE BOUND
 
Authors :  B. Stec
Date :  04 May 12  (Deposition) - 14 Nov 12  (Release) - 12 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (8x)
Keywords :  Catalytic Domain Tim Barrel, Carboxylase/Oxygenase, Nitrosylation, Chloroplast, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Stec
Structural Mechanism Of Rubisco Activation By Carbamylation Of The Active Site Lysine.
Proc. Natl. Acad. Sci. Usa V. 109 18785 2012
PubMed-ID: 23112176  |  Reference-DOI: 10.1073/PNAS.1210754109

(-) Compounds

Molecule 1 - RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
    Chains: A
    EC Number: 4.1.1.39
    Organism Common: RED ALGA
    Organism Scientific: GALDIERIA SULPHURARIA
    Organism Taxid: 130081
    Synonym: RUBISCO LARGE SUBUNIT
 
Molecule 2 - RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
    Chains: B
    EC Number: 4.1.1.39
    Organism Common: RED ALGA
    Organism Scientific: GALDIERIA SULPHURARIA
    Organism Taxid: 130081
    Synonym: RUBISCO SMALL SUBUNIT

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (8x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3MG1Ligand/IonMAGNESIUM ION
4SNC2Mod. Amino AcidS-NITROSO-CYSTEINE
Biological Unit 1 (2, 40)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL24Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4SNC16Mod. Amino AcidS-NITROSO-CYSTEINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:302 , HOH A:702 , HOH A:735 , HOH A:751BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREGLN A:312 , LYS A:313 , ASN A:314 , HIS A:315BINDING SITE FOR RESIDUE GOL A 502
3AC3SOFTWAREGLN B:614BINDING SITE FOR RESIDUE CL B 701
4AC4SOFTWAREARG A:170 , PHE A:229 , HOH A:810 , ARG B:544 , HOH B:809 , HOH B:816 , HOH B:821BINDING SITE FOR RESIDUE GOL B 702
5AC5SOFTWAREALA A:239 , ALA A:240 , HOH A:761 , PRO B:607 , PHE B:609 , TYR B:628 , GLU B:634BINDING SITE FOR RESIDUE GOL B 703

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F0M)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:184 -Pro A:185

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F0M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F0M)

(-) Exons   (0, 0)

(no "Exon" information available for 4F0M)

(-) 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:448
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4f0ma1 A:27-158 automated matches                                                                                                  d4f0ma2 A:159-474 automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeeeeeee....hhhhhhhhhhhhh.......hhhhhhhhhhhhh.eeeeeee.......eeeeeeehhhhh...hhhhhhhhhhh.......eeeeeeeeee.hhhhhh.......hhhhhhhhhh.....eee.........hhhhhhhhhhhhhhhh..eee...........hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh..eeeee.............eehhhhhhhhhhhhh..eee..........hhhhhhhhhhhhhh.ee..hhhhh....ee.......eeeee...hhhhhhhhhhhhh...eee.hhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f0m A  27 PYAKMGYWNPDYQVKDTDVLALFRVTPQPGVDPIEAAAAVAGESSTATWTVVWTDLLTAADLYRAKAYKVDQVPNNPEQYFAYIAYELDLFEEGSIANLTASIIGNVFGFKAVKALRLEDMRLPFAYIKTFQGPATGVILERERLDKFGRPLLGcTTKPKLGLSGKNYGRVVYEALKGGLDFVKDDENINSQPFMRWRERYLFVMEAVNKAAAATGEVKGHYLNVTAATMEEMYARAQLAKELGSVIIMIDLVIGYTAIQTMAKWARDNDMILHLHRAGNSTYSRQKNHGMNFRVICKWMRMAGVDHIHAGTVVGKLEGDPIITRGFYKTLLLPKLERNLQEGLFFDMDWASLRKVMPVASGGIHAGQMHQLIHYLGEDVVLQFGGGTIGHPDGIQSGATANRVALEAMILARNENRDFLTEGPEILREAAKNcGALRTALDLWKDIT 474
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176    |  186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456   |   466        
                                                                                                                                                                                    181-SNC                                                                                                                                                                                                                                                                                460-SNC          


Chain B from PDB  Type:PROTEIN  Length:138
                                                                                                                                                                          
               SCOP domains d4f0mb_ B: automated matches                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhh..eeeeeee..........ee..........hhhhhhhhhhhhhhh...eeeeeeee......eeeeeeeee.......eeeeeee.....eeeeeee.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4f0m B 501 MRITQGTFSFLPDLTDEQIKKQIDYMISKKLAIGIEYTNDIHPRNSFWEMWGLPLFEVTDPAPVLFEINACRKAKSNFYIKVVGFSSERGIESTIISFIVNRPKHEPGFNLIRQEDKSRSIKYSIQAYETYKPEDQRY 638
                                   510       520       530       540       550       560       570       580       590       600       610       620       630
   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  (3, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F0M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F0M)

(-) Gene Ontology  (12, 22)

Asymmetric Unit(hide GO term definitions)

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    Lys A:184 - Pro A:185   [ RasMol ]  
 
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  4f0m
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  RBL_GALSU | P23755
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  RBS_GALSU | P23756
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  4.1.1.39
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 Related Entries

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

UniProtKB/Swiss-Prot
        RBL_GALSU | P23755: 4f0h 4f0k
        RBS_GALSU | P23756: 4f0h 4f0k

(-) Related Entries Specified in the PDB File

4f0h 4f0k