1SW5 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PROX FROM ARCHEOGLOBUS FULGIDUS IN THE LIGAND FREE FORM

Authors :   A. Schiefner, G. Holtmann, K. Diederichs, W. Welte, E. Bremer

Date :   30 Mar 04 (Deposition) - 14 Sep 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Binding-Protein, Compatible Solutes, Cation-Pi Interactions, Non- Classical Hydrogen Bonds, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Schiefner, G. Holtmann, K. Diederichs, W. Welte, E. Bremer
Structural Basis For The Binding Of Compatible Solutes By Prox From The Hyperthermophilic Archaeon Archaeoglobus Fulgidus.
J. Biol. Chem. V. 279 48270 2004
PubMed-ID: 15308642 | Reference-DOI: 10.1074/JBC.M403540200

Molecule 1 - OSMOPROTECTION PROTEIN (PROX)
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PASK-IBA6
	Expression System Strain	:	BL21(CODON PLUS RIL)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PROX
	Mutation	:	YES
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	224325
	Strain	:	DSM 4304

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 9)

No.	Name	Count	Type	Full Name
1	CL	8	Ligand/Ion	CHLORIDE ION
2	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:74 , GLN A:75 , LYS B:74 , GLN B:75	BINDING SITE FOR RESIDUE CL B 401
2	AC2	SOFTWARE	LYS C:74 , GLN C:75 , LYS D:74 , GLN D:75	BINDING SITE FOR RESIDUE CL D 402
3	AC3	SOFTWARE	GLY A:44 , THR A:45 , LEU A:46 , VAL A:47 , GLY B:44 , THR B:45 , LEU B:46 , VAL B:47	BINDING SITE FOR RESIDUE CL A 403
4	AC4	SOFTWARE	GLY C:44 , THR C:45 , LEU C:46 , VAL C:47 , GLY D:44 , THR D:45 , LEU D:46 , VAL D:47	BINDING SITE FOR RESIDUE CL C 404
5	AC5	SOFTWARE	ASN A:69 , TYR A:214	BINDING SITE FOR RESIDUE CL A 405
6	AC6	SOFTWARE	ASN B:69 , TYR B:214	BINDING SITE FOR RESIDUE CL B 406
7	AC7	SOFTWARE	ASN C:69 , TYR C:214 , HOH C:446	BINDING SITE FOR RESIDUE CL C 407
8	AC8	SOFTWARE	ASN D:69 , TYR D:214	BINDING SITE FOR RESIDUE CL D 408
9	AC9	SOFTWARE	ASP A:244 , HOH A:420 , HOH A:446 , HOH A:492 , HOH A:503	BINDING SITE FOR RESIDUE MG A 409

(no "SS Bond" information available for 1SW5)

(no "Cis Peptide Bond" information available for 1SW5)

(no "SAP(SNP)/Variant" information available for 1SW5)

(no "PROSITE Motif" information available for 1SW5)

(no "Exon" information available for 1SW5)

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:270
 aligned with O29280_ARCFU | O29280 from UniProtKB/TrEMBL  Length:292

    Alignment length:270
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
         O29280_ARCFU    23 ERVVIGSKPFNEQYILANMIAILLEENGYKAEVKEGLGGTLVNYEALKRNDIQLYVEYTGTAYNVILRKQPPELWDQQYIFDEVKKGLLEADGVVVAAKLGFRDDYALAVRADWAEENGVEKISDLAEFADQLVFGSDPEFASRPDGLPQIKKVYGFEFKEVKQMEPTLMYEAIKNKQVDVIPAYTTDSRVDLFNLKILEDDKGALPPYDAIIIVNGNTAKDEKLISVLKLLEDRIDTDTMRALNYQYDVEKKDAREIAMSFLKEQGLVK 292
               SCOP domains d1sw5a_ A: Osmoprotection protein ProX                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1sw5A01 A:6-109,A:214-275 Periplasmic binding protein-like II                                           1sw5A02 A:110-213 Osmoprotection protein (prox); domain 2                                               1sw5A01 A:6-109,A:214-275 Periplasmic binding protein-like II  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee....hhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhh....eeeeehhhhhhh..........hhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeeeehhhhhhhh..hhhhhh.hhhh.eeeehhhhhhh..hhhhhhhhhh....eeee.hhhhhhhhhhh....eeeee..hhhhhhh.eee...........eeeeee..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sw5 A   6 ERVVIGSKPFNEQYILANMIAILLEENGYKAEVKEGLGGTLVNYEALKRNDIQLYVEYTGTAYNVILRKQPPELWDQQYIFDEVKKGLLEADGVVVAAKLGFRDDYALAVRADWAEENGVEKISDLAEFADQLVFGSDPEFASRPDGLPQIKKVYGFEFKEVKQMEPTLMYEAIKNKQVDVIPAYTTDSRVDLFNLKILEDDKGALPPYDAIIIVNGNTAKDEKLISVLKLLEDRIDTDTMRALNYQYDVEKKDAREIAMSFLKEQGLVK 275
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275

Chain B from PDB  Type:PROTEIN  Length:270
 aligned with O29280_ARCFU | O29280 from UniProtKB/TrEMBL  Length:292

    Alignment length:270
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
         O29280_ARCFU    23 ERVVIGSKPFNEQYILANMIAILLEENGYKAEVKEGLGGTLVNYEALKRNDIQLYVEYTGTAYNVILRKQPPELWDQQYIFDEVKKGLLEADGVVVAAKLGFRDDYALAVRADWAEENGVEKISDLAEFADQLVFGSDPEFASRPDGLPQIKKVYGFEFKEVKQMEPTLMYEAIKNKQVDVIPAYTTDSRVDLFNLKILEDDKGALPPYDAIIIVNGNTAKDEKLISVLKLLEDRIDTDTMRALNYQYDVEKKDAREIAMSFLKEQGLVK 292
               SCOP domains d1sw5b_ B: Osmoprotection protein ProX                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1sw5B01 B:6-109,B:214-275 Periplasmic binding protein-like II                                           1sw5B02 B:110-213 Osmoprotection protein (prox); domain 2                                               1sw5B01 B:6-109,B:214-275 Periplasmic binding protein-like II  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee....hhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhh....eeeeehhhhhhh..........hhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeeeehhhhhhh...hhhhhh.hhhh.eeeehhhhhhh..hhhhhhhhhh....eeee....hhhhhhhh.....eeee..hhhhhhh.eee...........eeeeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sw5 B   6 ERVVIGSKPFNEQYILANMIAILLEENGYKAEVKEGLGGTLVNYEALKRNDIQLYVEYTGTAYNVILRKQPPELWDQQYIFDEVKKGLLEADGVVVAAKLGFRDDYALAVRADWAEENGVEKISDLAEFADQLVFGSDPEFASRPDGLPQIKKVYGFEFKEVKQMEPTLMYEAIKNKQVDVIPAYTTDSRVDLFNLKILEDDKGALPPYDAIIIVNGNTAKDEKLISVLKLLEDRIDTDTMRALNYQYDVEKKDAREIAMSFLKEQGLVK 275
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275

Chain C from PDB  Type:PROTEIN  Length:270
 aligned with O29280_ARCFU | O29280 from UniProtKB/TrEMBL  Length:292

    Alignment length:270
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
         O29280_ARCFU    23 ERVVIGSKPFNEQYILANMIAILLEENGYKAEVKEGLGGTLVNYEALKRNDIQLYVEYTGTAYNVILRKQPPELWDQQYIFDEVKKGLLEADGVVVAAKLGFRDDYALAVRADWAEENGVEKISDLAEFADQLVFGSDPEFASRPDGLPQIKKVYGFEFKEVKQMEPTLMYEAIKNKQVDVIPAYTTDSRVDLFNLKILEDDKGALPPYDAIIIVNGNTAKDEKLISVLKLLEDRIDTDTMRALNYQYDVEKKDAREIAMSFLKEQGLVK 292
               SCOP domains d1sw5c_ C: Osmoprotection protein ProX                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1sw5C01 C:6-109,C:214-275 Periplasmic binding protein-like II                                           1sw5C02 C:110-213 Osmoprotection protein (prox); domain 2                                               1sw5C01 C:6-109,C:214-275 Periplasmic binding protein-like II  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhh....eeeeehhhhhhh..........hhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeeeehhhhhhhh..hhhhhhhhhhh.eeeehhhhhhh..hhhhhhhhh.....eeee.hhhhhhhhhhh....eeeee..hhhhhhh.eee...........eeeeee..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sw5 C   6 ERVVIGSKPFNEQYILANMIAILLEENGYKAEVKEGLGGTLVNYEALKRNDIQLYVEYTGTAYNVILRKQPPELWDQQYIFDEVKKGLLEADGVVVAAKLGFRDDYALAVRADWAEENGVEKISDLAEFADQLVFGSDPEFASRPDGLPQIKKVYGFEFKEVKQMEPTLMYEAIKNKQVDVIPAYTTDSRVDLFNLKILEDDKGALPPYDAIIIVNGNTAKDEKLISVLKLLEDRIDTDTMRALNYQYDVEKKDAREIAMSFLKEQGLVK 275
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275

Chain D from PDB  Type:PROTEIN  Length:270
 aligned with O29280_ARCFU | O29280 from UniProtKB/TrEMBL  Length:292

    Alignment length:270
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
         O29280_ARCFU    23 ERVVIGSKPFNEQYILANMIAILLEENGYKAEVKEGLGGTLVNYEALKRNDIQLYVEYTGTAYNVILRKQPPELWDQQYIFDEVKKGLLEADGVVVAAKLGFRDDYALAVRADWAEENGVEKISDLAEFADQLVFGSDPEFASRPDGLPQIKKVYGFEFKEVKQMEPTLMYEAIKNKQVDVIPAYTTDSRVDLFNLKILEDDKGALPPYDAIIIVNGNTAKDEKLISVLKLLEDRIDTDTMRALNYQYDVEKKDAREIAMSFLKEQGLVK 292
               SCOP domains d1sw5d_ D: Osmoprotection protein ProX                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1sw5D01 D:6-109,D:214-275 Periplasmic binding protein-like II                                           1sw5D02 D:110-213 Osmoprotection protein (prox); domain 2                                               1sw5D01 D:6-109,D:214-275 Periplasmic binding protein-like II  CATH domains
           Pfam domains (1) OpuAC-1sw5D01 D:6-270                                                                                                                                                                                                                                                    ----- Pfam domains (1)
           Pfam domains (2) OpuAC-1sw5D02 D:6-270                                                                                                                                                                                                                                                    ----- Pfam domains (2)
           Pfam domains (3) OpuAC-1sw5D03 D:6-270                                                                                                                                                                                                                                                    ----- Pfam domains (3)
           Pfam domains (4) OpuAC-1sw5D04 D:6-270                                                                                                                                                                                                                                                    ----- Pfam domains (4)
         Sec.struct. author ..eee....hhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhh....eeeeehhhhhhh..........hhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeeeehhhhhhh...hhhhhhhhhhh.eeeehhhhhhh..hhhhhhhhh.....eeee.hhhhhhhhhhh....eeeee...hhhhhh.eee...........eeeeee..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sw5 D   6 ERVVIGSKPFNEQYILANMIAILLEENGYKAEVKEGLGGTLVNYEALKRNDIQLYVEYTGTAYNVILRKQPPELWDQQYIFDEVKKGLLEADGVVVAAKLGFRDDYALAVRADWAEENGVEKISDLAEFADQLVFGSDPEFASRPDGLPQIKKVYGFEFKEVKQMEPTLMYEAIKNKQVDVIPAYTTDSRVDLFNLKILEDDKGALPPYDAIIIVNGNTAKDEKLISVLKLLEDRIDTDTMRALNYQYDVEKKDAREIAMSFLKEQGLVK 275
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Periplasmic binding protein-like II (813)

Superfamily: Periplasmic binding protein-like II (813)

Family: Phosphate binding protein-like (463)

Protein domain: Osmoprotection protein ProX (5)

Archaeoglobus fulgidus [TaxId: 2234] (5)

1a	d1sw5a_	A:
1b	d1sw5b_	B:
1c	d1sw5c_	C:
1d	d1sw5d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: D-Maltodextrin-Binding Protein; domain 2 (600)

Homologous Superfamily: Osmoprotection protein (prox); domain 2 (4)

Archaeoglobus fulgidus dsm 4304. Organism_taxid: 224325. Strain: dsm 4304. (4)

1a	1sw5A02	A:110-213
1b	1sw5B02	B:110-213
1c	1sw5C02	C:110-213
1d	1sw5D02	D:110-213

Homologous Superfamily: Periplasmic binding protein-like II (486)

Archaeoglobus fulgidus dsm 4304. Organism_taxid: 224325. Strain: dsm 4304. (4)

2a	1sw5A01	A:6-109,A:214-275
2b	1sw5B01	B:6-109,B:214-275
2c	1sw5C01	C:6-109,C:214-275
2d	1sw5D01	D:6-109,D:214-275

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PBP (391)

Family: OpuAC (18)

Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (5)

1a	OpuAC-1sw5D01	D:6-270
1b	OpuAC-1sw5D02	D:6-270
1c	OpuAC-1sw5D03	D:6-270
1d	OpuAC-1sw5D04	D:6-270

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (O29280_ARCFU | O29280)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005215	transporter activity	Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

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	1sw5
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	O29280_ARCFU \| O29280	:	1sw1 1sw2 1sw4 3mam

1sw1	CRYSTAL STRUCTURE OF PROX FROM ARCHEOGLOBUS FULGIDUS IN COMPLEX WITH PROLINE BETAINE
1sw2	CRYSTAL STRUCTURE OF PROX FROM ARCHEOGLOBUS FULGIDUS IN COMPLEX WITH GLYCINE BETAINE
1sw4	CRYSTAL STRUCTURE OF PROX FROM ARCHEOGLOBUS FULGIDUS IN COMPLEX WITH TRIMETHYL AMMONIUM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 9)

Sites (9, 9)

SS Bonds (0, 0)

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