1A4C - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   AZURIN MUTANT WITH MET 121 REPLACED BY HIS, PH 3.5 CRYSTAL FORM, DATA COLLECTED AT-180 DEGREES CELSIUS

Authors :   A. Messerschmidt, L. Prade

Date :   28 Jan 98 (Deposition) - 29 Apr 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

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

Keywords :   Electron Transport, Cuproprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Messerschmidt, L. Prade, S. J. Kroes, J. Sanders-Loehr, R. Huber, G. W. Canters
Rack-Induced Metal Binding Vs. Flexibility: Met121His Azurin Crystal Structures At Different Ph.
Proc. Natl. Acad. Sci. Usa V. 95 3443 1998
PubMed-ID: 9520385 | Reference-DOI: 10.1073/PNAS.95.7.3443
(for further references see the PDB file header)

Molecule 1 - AZURIN
	Cellular Location	:	PERIPLASM
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	AZU
	Expression System Plasmid	:	PCH11
	Expression System Strain	:	JM101
	Expression System Taxid	:	562
	Gene	:	AZU
	Mutation	:	YES
	Organism Scientific	:	ACHROMOBACTER DENITRIFICANS
	Organism Taxid	:	32002

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	CU	4	Ligand/Ion	COPPER (II) ION
2	NO3	2	Ligand/Ion	NITRATE ION
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	NO3	1	Ligand/Ion	NITRATE ION
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	NO3	1	Ligand/Ion	NITRATE ION
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:46 , CYS A:112 , HIS A:117 , HIS A:121	BINDING SITE FOR RESIDUE CU A 130
02	AC2	SOFTWARE	GLY A:76 , HIS A:83 , HOH A:212 , HOH A:226	BINDING SITE FOR RESIDUE SO4 A 131
03	AC3	SOFTWARE	HIS B:46 , CYS B:112 , HIS B:117 , HIS B:121	BINDING SITE FOR RESIDUE CU B 130
04	AC4	SOFTWARE	VAL B:73 , ALA B:75 , GLY B:76 , HIS B:83 , HOH B:147 , HOH B:232	BINDING SITE FOR RESIDUE SO4 B 131
05	AC5	SOFTWARE	GLY C:45 , HIS C:46 , CYS C:112 , HIS C:117 , NO3 C:132	BINDING SITE FOR RESIDUE CU C 130
06	AC6	SOFTWARE	VAL C:73 , LYS C:74 , ALA C:75 , GLY C:76 , HIS C:83 , HOH C:154 , HOH C:222	BINDING SITE FOR RESIDUE SO4 C 131
07	AC7	SOFTWARE	MET C:13 , GLN C:14 , HIS C:46 , CYS C:112 , HIS C:117 , HIS C:121 , CU C:130	BINDING SITE FOR RESIDUE NO3 C 132
08	AC8	SOFTWARE	GLY D:45 , HIS D:46 , CYS D:112 , HIS D:117 , NO3 D:132	BINDING SITE FOR RESIDUE CU D 130
09	AC9	SOFTWARE	ALA D:75 , GLY D:76 , HIS D:83 , HOH D:176 , HOH D:236	BINDING SITE FOR RESIDUE SO4 D 131
10	BC1	SOFTWARE	SER D:9 , MET D:13 , GLN D:14 , TYR D:15 , HIS D:46 , CYS D:112 , HIS D:117 , HIS D:121 , CU D:130	BINDING SITE FOR RESIDUE NO3 D 132

Asymmetric Unit

No.	Residues
1	A:3	-	A:26
2	B:3	-	B:26
3	C:3	-	C:26
4	D:3	-	D:26

(no "Cis Peptide Bond" information available for 1A4C)

(no "SAP(SNP)/Variant" information available for 1A4C)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AZUR_ACHDE	125-141	4	A:105-120 B:105-120 C:105-120 D:105-120

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AZUR_ACHDE	125-141	2	A:105-120 - C:105-120 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	AZUR_ACHDE	125-141	2	- B:105-120 - D:105-120

(no "Exon" information available for 1A4C)

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:129
 aligned with AZUR_ACHDE | P00280 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:129
                                    30        40        50        60        70        80        90       100       110       120       130       140         
           AZUR_ACHDE    21 AQCEATIESNDAMQYNLKEMVVDKSCKQFTVHLKHVGKMAKVAMGHNWVLTKEADKQGVATDGMNAGLAQDYVKAGDTRVIAHTKVIGGGESDSVTFDVSKLTPGEAYAYFCSFPGHWAMMKGTLKLSN 149
               SCOP domains d1a4ca_ A: Azurin                                                                                                                 SCOP domains
               CATH domains 1a4cA00 A:1-129 Cupredoxins -  blue copper proteins                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ..eeeeeeee...eee.eeeee....eeeeeeeeee.........eeeeee...hhhhhhhhhhhhh.............eeeeeee...-------hhhhh.....eeeee........eeeeeeee. Sec.struct. author (1)
     Sec.struct. author (2) ------------------------------------------------------------------------------------------eeeeeeeee------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      -------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a4c A   1 AQCEATIESNDAMQYDLKEMVVDKSCKQFTVHLKHVGKMAKSAMGHNWVLTKEADKEGVATDGMNAGLAQDYVKAGDTRVIAHTKVIGGGESDSVTFDVSKLTPGEAYAYFCSFPGHWAMHKGTLKLSN 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:129
 aligned with AZUR_ACHDE | P00280 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:129
                                    30        40        50        60        70        80        90       100       110       120       130       140         
           AZUR_ACHDE    21 AQCEATIESNDAMQYNLKEMVVDKSCKQFTVHLKHVGKMAKVAMGHNWVLTKEADKQGVATDGMNAGLAQDYVKAGDTRVIAHTKVIGGGESDSVTFDVSKLTPGEAYAYFCSFPGHWAMMKGTLKLSN 149
               SCOP domains d1a4cb_ B: Azurin                                                                                                                 SCOP domains
               CATH domains 1a4cB00 B:1-129 Cupredoxins -  blue copper proteins                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ..eeeeeeee...eee.eeeee....eeeeeeeeee.........eeeeee...hhhhhhhhhhhhh.............eeeeeee...-------hhhhh.....eeeee........eeeeeeee. Sec.struct. author (1)
     Sec.struct. author (2) ------------------------------------------------------------------------------------------eeeeeeeee------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      -------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a4c B   1 AQCEATIESNDAMQYDLKEMVVDKSCKQFTVHLKHVGKMAKSAMGHNWVLTKEADKEGVATDGMNAGLAQDYVKAGDTRVIAHTKVIGGGESDSVTFDVSKLTPGEAYAYFCSFPGHWAMHKGTLKLSN 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:129
 aligned with AZUR_ACHDE | P00280 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:129
                                    30        40        50        60        70        80        90       100       110       120       130       140         
           AZUR_ACHDE    21 AQCEATIESNDAMQYNLKEMVVDKSCKQFTVHLKHVGKMAKVAMGHNWVLTKEADKQGVATDGMNAGLAQDYVKAGDTRVIAHTKVIGGGESDSVTFDVSKLTPGEAYAYFCSFPGHWAMMKGTLKLSN 149
               SCOP domains d1a4cc_ C: Azurin                                                                                                                 SCOP domains
               CATH domains 1a4cC00 C:1-129 Cupredoxins -  blue copper proteins                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ..eeeeeeee...eee.eeeee....eeeeeeeeee.........eeeeee...hhhhhhhhhhhhh.............eeeeeee...-------hhhhh.....eeeee........eeeeeeee. Sec.struct. author (1)
     Sec.struct. author (2) ------------------------------------------------------------------------------------------eeeeeeeee------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      -------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a4c C   1 AQCEATIESNDAMQYDLKEMVVDKSCKQFTVHLKHVGKMAKSAMGHNWVLTKEADKEGVATDGMNAGLAQDYVKAGDTRVIAHTKVIGGGESDSVTFDVSKLTPGEAYAYFCSFPGHWAMHKGTLKLSN 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain D from PDB  Type:PROTEIN  Length:129
 aligned with AZUR_ACHDE | P00280 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:129
                                    30        40        50        60        70        80        90       100       110       120       130       140         
           AZUR_ACHDE    21 AQCEATIESNDAMQYNLKEMVVDKSCKQFTVHLKHVGKMAKVAMGHNWVLTKEADKQGVATDGMNAGLAQDYVKAGDTRVIAHTKVIGGGESDSVTFDVSKLTPGEAYAYFCSFPGHWAMMKGTLKLSN 149
               SCOP domains d1a4cd_ D: Azurin                                                                                                                 SCOP domains
               CATH domains 1a4cD00 D:1-129 Cupredoxins -  blue copper proteins                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ..eeeeeeee...eee.eeeee....eeeeeeeeee.........eeeeee...hhhhhhhhhhhhh.............eeeeeee...-------hhhhh.....eeeee........eeeeeeee. Sec.struct. author (1)
     Sec.struct. author (2) ------------------------------------------------------------------------------------------eeeeeeeee------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------COPPER_BLUE      -------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a4c D   1 AQCEATIESNDAMQYDLKEMVVDKSCKQFTVHLKHVGKMAKSAMGHNWVLTKEADKEGVATDGMNAGLAQDYVKAGDTRVIAHTKVIGGGESDSVTFDVSKLTPGEAYAYFCSFPGHWAMHKGTLKLSN 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

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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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Cupredoxin-like (545)

Superfamily: Cupredoxins (543)

Family: Plastocyanin/azurin-like (241)

Protein domain: Azurin (95)

Alcaligenes denitrificans [TaxId: 32002] (8)

1a	d1a4ca_	A:
1b	d1a4cb_	B:
1c	d1a4cc_	C:
1d	d1a4cd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Cupredoxins - blue copper proteins (420)

Achromobacter denitrificans. Organism_taxid: 32002. (3)

1a	1a4cA00	A:1-129
1b	1a4cB00	B:1-129
1c	1a4cC00	C:1-129
1d	1a4cD00	D:1-129

(no "Pfam Domain" information available for 1A4C)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (AZUR_ACHDE | P00280)

molecular function
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric Unit
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	1a4c
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	AZUR_ACHDE \| P00280	:	1a4a 1a4b 1aiz 1azb 1azc 1uri 2aza

(no "Related Entries Specified in the PDB File" available for 1A4C)

Description

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SS Bonds (4, 4)

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