2R50 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF NONSYMBIOTIC CORN HEMOGLOBIN 1

Authors :   B. J. Smagghe, J. A. Hoy, M. S. Hargrove

Date :   02 Sep 07 (Deposition) - 18 Sep 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,D  (1x)
Biol. Unit 2: B,C  (1x)
Biol. Unit 3: A,B,C,D  (1x)

Keywords :   Corn Hemoglobin, Plant Hemoglobin, Nonsymbiotic Hemoglobin, Heme, Iron, Metal-Binding, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. J. Smagghe, J. A. Hoy, M. S. Hargrove
The Crystal Structure Of Nonsymbiotic Corn Hemoglobin 1
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - NON-SYMBIOTIC HEMOGLOBIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21* DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HB, GLB1
	Organism Scientific	:	ZEA MAYS SUBSP. PARVIGLUMIS
	Organism Taxid	:	76912
	Strain	:	SUBSP. PARVIGLUMIS
	Synonym	:	HBT, ZEAMP GLB1

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A			D
Biological Unit 2 (1x)	:		B	C
Biological Unit 3 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 11)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 11)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG B:110 , TYR B:111 , HOH B:204 , HOH B:205 , PRO C:163 , ASP C:164 , HOH C:195	BINDING SITE FOR RESIDUE SO4 B 166
02	AC2	SOFTWARE	ASP B:164 , HOH B:304 , ARG C:110 , TYR C:111	BINDING SITE FOR RESIDUE SO4 C 166
03	AC3	SOFTWARE	LYS C:130 , TRP C:138 , LYS C:143 , HOH C:276 , HOH C:281	BINDING SITE FOR RESIDUE SO4 C 167
04	AC4	SOFTWARE	ARG A:110 , TYR A:111 , LYS D:162 , PRO D:163 , ASP D:164	BINDING SITE FOR RESIDUE SO4 D 166
05	AC5	SOFTWARE	ASP A:164 , ARG D:110 , TYR D:111 , HOH D:230	BINDING SITE FOR RESIDUE SO4 D 167
06	AC6	SOFTWARE	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 , HIS A:117 , THR A:121 , ILE A:157 , HOH A:212 , HOH A:326	BINDING SITE FOR RESIDUE HEM A 166
07	AC7	SOFTWARE	MET B:53 , PHE B:54 , LYS B:69 , HIS B:73 , ARG B:103 , LEU B:104 , HIS B:108 , TYR B:111 , HIS B:117 , THR B:121 , HOH B:191 , HOH B:283	BINDING SITE FOR RESIDUE HEM B 167
08	AC8	SOFTWARE	MET C:53 , PHE C:56 , HIS C:73 , ARG C:103 , LEU C:104 , THR C:107 , HIS C:108 , TYR C:111 , HIS C:117 , THR C:121 , LEU C:153 , HOH C:224	BINDING SITE FOR RESIDUE HEM C 168
09	AC9	SOFTWARE	LYS D:69 , HIS D:73 , MET D:80 , ARG D:103 , LEU D:104 , THR D:107 , HIS D:108 , TYR D:111 , VAL D:113 , HIS D:117 , THR D:121	BINDING SITE FOR RESIDUE HEM D 168
10	BC1	SOFTWARE	PHE B:39 , PHE B:40 , HIS B:73 , ALA B:74 , VAL B:77 , HOH B:176	BINDING SITE FOR RESIDUE ACY B 168
11	BC2	SOFTWARE	PHE D:40 , HIS D:73 , ALA D:74 , VAL D:77 , HOH D:173	BINDING SITE FOR RESIDUE ACY D 169

(no "SS Bond" information available for 2R50)

(no "Cis Peptide Bond" information available for 2R50)

(no "SAP(SNP)/Variant" information available for 2R50)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	HBL_ZEAMP	13-162	4	A:13-162 B:13-162 C:13-162 D:13-162
2	PLANT_GLOBIN	PS00208	Plant hemoglobins signature.	HBL_ZEAMP	67-78	4	A:67-78 B:67-78 C:67-78 D:67-78

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	HBL_ZEAMP	13-162	2	A:13-162 - - D:13-162
2	PLANT_GLOBIN	PS00208	Plant hemoglobins signature.	HBL_ZEAMP	67-78	2	A:67-78 - - D:67-78

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	HBL_ZEAMP	13-162	2	- B:13-162 C:13-162 -
2	PLANT_GLOBIN	PS00208	Plant hemoglobins signature.	HBL_ZEAMP	67-78	2	- B:67-78 C:67-78 -

Biological Unit 3 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLOBIN	PS01033	Globin family profile.	HBL_ZEAMP	13-162	4	A:13-162 B:13-162 C:13-162 D:13-162
2	PLANT_GLOBIN	PS00208	Plant hemoglobins signature.	HBL_ZEAMP	67-78	4	A:67-78 B:67-78 C:67-78 D:67-78

(no "Exon" information available for 2R50)

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:146
 aligned with HBL_ZEAMP | Q9M593 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:155
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     
            HBL_ZEAMP    11 VVFGEEQEALVLKSWAVMKKDAANLGLRFFLKVFEIAPSAKQMFSFLRDSDVPLEKNPKLKTHAMSVFVMTCEAAAQLRKAGKVTVRETTLKRLGATHLRYGVADGHFEVTGFALLETIKEALPADMWSLEMKKAWAEAYSQLVAAIKREMKPDA 165
               SCOP domains d2r50a_ A: automated matches                                                                                                                                SCOP domains
               CATH domains 2r50A00 A:11-165 Globins                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh---------...hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --GLOBIN  PDB: A:13-162 UniProt: 13-162                                                                                                                 --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------PLANT_GLOBIN--------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r50 A  11 VVFGEEQEALVLKSWAVMKKDAANLGLRFFLKVFEIAPSAKQMF---------LEKNPKLKTHAMSVFVMTCEAAAQLRKAGKVTVRETTLKRLGATHLRYGVADGHFEVTGFALLETIKEALPADMWSLEMKKAWAEAYSQLVAAIKREMKPDA 165
                                    20        30        40        50   |     -   |    70        80        90       100       110       120       130       140       150       160     
                                                                      54        64

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with HBL_ZEAMP | Q9M593 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:155
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     
            HBL_ZEAMP    11 VVFGEEQEALVLKSWAVMKKDAANLGLRFFLKVFEIAPSAKQMFSFLRDSDVPLEKNPKLKTHAMSVFVMTCEAAAQLRKAGKVTVRETTLKRLGATHLRYGVADGHFEVTGFALLETIKEALPADMWSLEMKKAWAEAYSQLVAAIKREMKPDA 165
               SCOP domains d2r50b_ B: automated matches                                                                                                                                SCOP domains
               CATH domains 2r50B00 B:11-165 Globins                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.---------...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --GLOBIN  PDB: B:13-162 UniProt: 13-162                                                                                                                 --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------PLANT_GLOBIN--------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r50 B  11 VVFGEEQEALVLKSWAVMKKDAANLGLRFFLKVFEIAPSAKQMFS---------EKNPKLKTHAMSVFVMTCEAAAQLRKAGKVTVRETTLKRLGATHLRYGVADGHFEVTGFALLETIKEALPADMWSLEMKKAWAEAYSQLVAAIKREMKPDA 165
                                    20        30        40        50    |    -    |   70        80        90       100       110       120       130       140       150       160     
                                                                       55        65

Chain C from PDB  Type:PROTEIN  Length:147
 aligned with HBL_ZEAMP | Q9M593 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:154
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
            HBL_ZEAMP    12 VFGEEQEALVLKSWAVMKKDAANLGLRFFLKVFEIAPSAKQMFSFLRDSDVPLEKNPKLKTHAMSVFVMTCEAAAQLRKAGKVTVRETTLKRLGATHLRYGVADGHFEVTGFALLETIKEALPADMWSLEMKKAWAEAYSQLVAAIKREMKPDA 165
               SCOP domains d2r50c_ C: automated matches                                                                                                                               SCOP domains
               CATH domains 2r50C00 C:12-165 Globins                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..-------...hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -GLOBIN  PDB: C:13-162 UniProt: 13-162                                                                                                                 --- PROSITE (1)
                PROSITE (2) -------------------------------------------------------PLANT_GLOBIN--------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r50 C  12 VFGEEQEALVLKSWAVMKKDAANLGLRFFLKVFEIAPSAKQMFSF-------LEKNPKLKTHAMSVFVMTCEAAAQLRKAGKVTVRETTLKRLGATHLRYGVADGHFEVTGFALLETIKEALPADMWSLEMKKAWAEAYSQLVAAIKREMKPDA 165
                                    21        31        41        51    |    -  |     71        81        91       101       111       121       131       141       151       161    
                                                                       56      64

Chain D from PDB  Type:PROTEIN  Length:145
 aligned with HBL_ZEAMP | Q9M593 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:154
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
            HBL_ZEAMP    12 VFGEEQEALVLKSWAVMKKDAANLGLRFFLKVFEIAPSAKQMFSFLRDSDVPLEKNPKLKTHAMSVFVMTCEAAAQLRKAGKVTVRETTLKRLGATHLRYGVADGHFEVTGFALLETIKEALPADMWSLEMKKAWAEAYSQLVAAIKREMKPDA 165
               SCOP domains d2r50d_ D: automated matches                                                                                                                               SCOP domains
               CATH domains 2r50D00 D:12-165 Globins                                                                                                                                   CATH domains
           Pfam domains (1) -----Globin-2r50D01 D:17-126                                                                                       --------------------------------------- Pfam domains (1)
           Pfam domains (2) -----Globin-2r50D02 D:17-126                                                                                       --------------------------------------- Pfam domains (2)
           Pfam domains (3) -----Globin-2r50D03 D:17-126                                                                                       --------------------------------------- Pfam domains (3)
           Pfam domains (4) -----Globin-2r50D04 D:17-126                                                                                       --------------------------------------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.---------..hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -GLOBIN  PDB: D:13-162 UniProt: 13-162                                                                                                                 --- PROSITE (1)
                PROSITE (2) -------------------------------------------------------PLANT_GLOBIN--------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r50 D  12 VFGEEQEALVLKSWAVMKKDAANLGLRFFLKVFEIAPSAKQMFS---------EKNPKLKTHAMSVFVMTCEAAAQLRKAGKVTVRETTLKRLGATHLRYGVADGHFEVTGFALLETIKEALPADMWSLEMKKAWAEAYSQLVAAIKREMKPDA 165
                                    21        31        41        51   |     -   |    71        81        91       101       111       121       131       141       151       161    
                                                                      55        65

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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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Globin-like (1351)

Superfamily: Globin-like (1308)

Family: Globins (1157)

Protein domain: automated matches (99)

Maize (Zea mays) [TaxId: 76912] (1)

1a	d2r50a_	A:
1b	d2r50b_	B:
1c	d2r50c_	C:
1d	d2r50d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Globin-like (786)

Homologous Superfamily: Globins (743)

Parviglumis (Zea mays subsp) (1)

1a	2r50D00	D:12-165
1b	2r50A00	A:11-165
1c	2r50B00	B:11-165
1d	2r50C00	C:12-165

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Globin (291)

Family: Globin (264)

Zea mays subsp. parviglumis (Balsas teosinte) (1)

1a	Globin-2r50D01	D:17-126
1b	Globin-2r50D02	D:17-126
1c	Globin-2r50D03	D:17-126
1d	Globin-2r50D04	D:17-126

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (HBL_ZEAMP | Q9M593)


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).

Asymmetric Unit
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Ligands, Modified Residues, Ions (3, 11)

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