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(-) Description

Title :  CRYSTAL STRUCTURE OF NON-SYMBIOTIC PLANT HEMOGLOBIN FROM RICE
 
Authors :  M. Hargrove, E. A. Brucker, B. Stec, J. S. Olson, G. N. Phillips Jr.
Date :  26 Oct 99  (Deposition) - 10 Jan 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Globin, Bis-Histidyl, Heme Protein, Oxygen Storage/Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. S. Hargrove, E. A. Brucker, B. Stec, G. Sarath, R. Arredondo-Peter, R. V. Klucas, J. S. Olson, G. N. Phillips Jr.
Crystal Structure Of A Nonsymbiotic Plant Hemoglobin.
Structure Fold. Des. V. 8 1005 2000
PubMed-ID: 10986467  |  Reference-DOI: 10.1016/S0969-2126(00)00194-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NON-SYMBIOTIC HEMOGLOBIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organ: ROOT
    Organism Common: RICE
    Organism Scientific: ORYZA SATIVA
    Organism Taxid: 4530

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:50 , MET A:53 , PHE A:54 , LYS A:69 , HIS A:73 , ARG A:103 , LEU A:104 , THR A:107 , HIS A:108 , TYR A:111 , VAL A:113 , HIS A:117 , PHE A:118 , VAL A:121 , LEU A:153 , VAL A:154 , HOH A:280BINDING SITE FOR RESIDUE HEM A 166
2AC2SOFTWAREMET B:53 , PHE B:54 , LYS B:69 , HIS B:73 , ARG B:103 , LEU B:104 , THR B:107 , HIS B:108 , TYR B:111 , VAL B:113 , HIS B:117 , PHE B:118 , VAL B:121 , LEU B:153 , VAL B:154 , HOH B:231BINDING SITE FOR RESIDUE HEM B 166

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1D8U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1D8U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1D8U)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLOBINPS01033 Globin family profile.HBL1_ORYSJ12-163
 		  2A:11-162
B:11-162
2PLANT_GLOBINPS00208 Plant hemoglobins signature.HBL1_ORYSJ68-79
 		  2A:67-78
B:67-78

(-) Exons   (0, 0)

(no "Exon" information available for 1D8U)

(-) Sequences/Alignments

Asymmetric/Biological 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:165
 aligned with HBL1_ORYSJ | O04986 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161     
           HBL1_ORYSJ     2 ALVEDNNAVAVSFSEEQEALVLKSWAILKKDSANIALRFFLKIFEVAPSASQMFSFLRNSDVPLEKNPKLKTHAMSVFVMTCEAAAQLRKAGKVTVRDTTLKRLGATHLKYGVGDAHFEVVKFALLDTIKEEVPADMWSPAMKSAWSEAYDHLVAAIKQEMKPAE 166
               SCOP domains d1d8ua_ A: Non-symbiotic plant hemoglobin                                                                                                                             SCOP domains
               CATH domains 1d8uA00 A:1-165 Globins                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------GLOBIN  PDB: A:11-162 UniProt: 12-163                                                                                                                   --- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------PLANT_GLOBIN--------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d8u A   1 ALVEDNNAVAVSFSEEQEALVLKSWAILKKDSANIALRFFLKIFEVAPSASQMFSFLRNSDVPLEKNPKLKTHAMSVFVMTCEAAAQLRKAGKVTVRDTTLKRLGATHLKYGVGDAHFEVVKFALLDTIKEEVPADMWSPAMKSAWSEAYDHLVAAIKQEMKPAE 165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     


Chain B from PDB  Type:PROTEIN  Length:165
 aligned with HBL1_ORYSJ | O04986 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161     
           HBL1_ORYSJ     2 ALVEDNNAVAVSFSEEQEALVLKSWAILKKDSANIALRFFLKIFEVAPSASQMFSFLRNSDVPLEKNPKLKTHAMSVFVMTCEAAAQLRKAGKVTVRDTTLKRLGATHLKYGVGDAHFEVVKFALLDTIKEEVPADMWSPAMKSAWSEAYDHLVAAIKQEMKPAE 166
               SCOP domains d1d8ub_ B: Non-symbiotic plant hemoglobin                                                                                                                             SCOP domains
               CATH domains 1d8uB00 B:1-165 Globins                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------GLOBIN  PDB: B:11-162 UniProt: 12-163                                                                                                                   --- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------PLANT_GLOBIN--------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d8u B   1 ALVEDNNAVAVSFSEEQEALVLKSWAILKKDSANIALRFFLKIFEVAPSASQMFSFLRNSDVPLEKNPKLKTHAMSVFVMTCEAAAQLRKAGKVTVRDTTLKRLGATHLKYGVGDAHFEVVKFALLDTIKEEVPADMWSPAMKSAWSEAYDHLVAAIKQEMKPAE 165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1D8U)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HBL1_ORYSJ | O04986)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0019825    oxygen binding    Interacting selectively and non-covalently with oxygen (O2).

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 Related Entries

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

UniProtKB/Swiss-Prot
        HBL1_ORYSJ | O04986: 2gnv 2gnw

(-) Related Entries Specified in the PDB File

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