1F4M - JenaLib

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Title :   P3(2) CRYSTAL STRUCTURE OF ALA2ILE2-6, A VERSION OF ROP WITH A REPACKED HYDROPHOBIC CORE AND A NEW FOLD.

Authors :   M. A. Willis, B. Bishop, L. Regan, A. T. Brunger

Date :   08 Jun 00 (Deposition) - 10 Jan 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   Rop, Dimer, Homodimer, Helix-Turn-Helix, Transcription Regulation, Hydrophobic Core Packing, Thermodynamic Stability (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Willis, B. Bishop, L. Regan, A. T. Brunger
Dramatic Structural And Thermodynamic Consequences Of Repacking A Protein'S Hydrophobic Core.
Structure Fold. Des. V. 8 1319 2000
PubMed-ID: 11188696 | Reference-DOI: 10.1016/S0969-2126(00)00544-X
(for further references see the PDB file header)

Molecule 1 - ROP ALA2ILE2-6
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	REGULATORY PROTEIN ROP, ROM

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	CA	6	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU C:39 , ASP C:43 , HOH C:106 , HOH C:113 , HOH C:114 , HOH C:122	BINDING SITE FOR RESIDUE CA C 101
2	AC2	SOFTWARE	HOH C:107 , HOH C:108 , HOH C:111 , HOH C:121 , GLU D:39 , ASP D:43	BINDING SITE FOR RESIDUE CA C 102
3	AC3	SOFTWARE	GLU A:39 , ASP A:43 , HOH A:108 , HOH A:109 , HOH A:110 , HOH A:111	BINDING SITE FOR RESIDUE CA A 103
4	AC4	SOFTWARE	HOH A:106 , HOH A:112 , HOH A:113 , GLU B:39 , ASP B:43	BINDING SITE FOR RESIDUE CA A 104
5	AC5	SOFTWARE	GLU E:39 , ASP E:43 , HOH E:108 , HOH E:109	BINDING SITE FOR RESIDUE CA E 105
6	AC6	SOFTWARE	HOH E:110 , GLU F:39 , ASP F:43 , HOH F:69	BINDING SITE FOR RESIDUE CA E 106

(no "SS Bond" information available for 1F4M)

(no "Cis Peptide Bond" information available for 1F4M)

(no "SAP(SNP)/Variant" information available for 1F4M)

(no "PROSITE Motif" information available for 1F4M)

(no "Exon" information available for 1F4M)

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:56
 aligned with ROP_ECOLX | P03051 from UniProtKB/Swiss-Prot  Length:63

    Alignment length:56
                                    10        20        30        40        50      
             ROP_ECOLX    1 MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHADELYRSCLARF 56
               SCOP domains d1f4ma_ A: ROP protein                                   SCOP domains
               CATH domains 1f4mA00 A:1-56  [code=1.10.287.230, no name defined]     CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                  1f4m A  1 GTKQEKTILNMARFIRSQALTILEKANELDADEIADIAESIHDHADEIYRSALARF 56
                                    10        20        30        40        50

Chain B from PDB  Type:PROTEIN  Length:56
 aligned with ROP_ECOLX | P03051 from UniProtKB/Swiss-Prot  Length:63

    Alignment length:56
                                    11        21        31        41        51      
             ROP_ECOLX    2 TKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHADELYRSCLARFG 57
               SCOP domains d1f4mb_ B: ROP protein                                   SCOP domains
               CATH domains 1f4mB00 B:2-57  [code=1.10.287.230, no name defined]     CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                  1f4m B  2 TKQEKTILNMARFIRSQALTILEKANELDADEIADIAESIHDHADEIYRSALARFG 57
                                    11        21        31        41        51

Chain C from PDB  Type:PROTEIN  Length:54
 aligned with ROP_ECOLX | P03051 from UniProtKB/Swiss-Prot  Length:63

    Alignment length:54
                                    11        21        31        41        51    
             ROP_ECOLX    2 TKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHADELYRSCLAR 55
               SCOP domains d1f4mc_ C: ROP protein                                 SCOP domains
               CATH domains 1f4mC00 C:2-55  [code=1.10.287.230, no name defined]   CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                  1f4m C  2 TKQEKTILNMARFIRSQALTILEKANELDADEIADIAESIHDHADEIYRSALAR 55
                                    11        21        31        41        51

Chain D from PDB  Type:PROTEIN  Length:57
 aligned with ROP_ECOLX | P03051 from UniProtKB/Swiss-Prot  Length:63

    Alignment length:57
                                    10        20        30        40        50       
             ROP_ECOLX    1 MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHADELYRSCLARFG 57
               SCOP domains d1f4md_ D: ROP protein                                    SCOP domains
               CATH domains 1f4mD00 D:1-57  [code=1.10.287.230, no name defined]      CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                  1f4m D  1 GTKQEKTILNMARFIRSQALTILEKANELDADEIADIAESIHDHADEIYRSALARFG 57
                                    10        20        30        40        50

Chain E from PDB  Type:PROTEIN  Length:53
 aligned with ROP_ECOLX | P03051 from UniProtKB/Swiss-Prot  Length:63

    Alignment length:53
                                    14        24        34        44        54   
             ROP_ECOLX    5 EKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHADELYRSCLARFG 57
               SCOP domains d1f4me_ E: ROP protein                                SCOP domains
               CATH domains 1f4mE00 E:5-57  [code=1.10.287.230, no name defined]  CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  1f4m E  5 EKTILNMARFIRSQALTILEKANELDADEIADIAESIHDHADEIYRSALARFG 57
                                    14        24        34        44        54

Chain F from PDB  Type:PROTEIN  Length:54
 aligned with ROP_ECOLX | P03051 from UniProtKB/Swiss-Prot  Length:63

    Alignment length:54
                                    13        23        33        43        53    
             ROP_ECOLX    4 QEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHADELYRSCLARFG 57
               SCOP domains d1f4mf_ F: ROP protein                                 SCOP domains
               CATH domains 1f4mF00 F:4-57  [code=1.10.287.230, no name defined]   CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                  1f4m F  4 QEKTILNMARFIRSQALTILEKANELDADEIADIAESIHDHADEIYRSALARFG 57
                                    13        23        33        43        53

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: All alpha proteins (14657)

Fold: ROP-like (34)

Superfamily: ROP protein (17)

Family: ROP protein (17)

Protein domain: ROP protein (17)

Escherichia coli [TaxId: 562] (17)

1a	d1f4ma_	A:
1b	d1f4mb_	B:
1c	d1f4mc_	C:
1d	d1f4md_	D:
1e	d1f4me_	E:
1f	d1f4mf_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Helix Hairpins (718)

Homologous Superfamily: [code=1.10.287.230, no name defined] (10)

Escherichia coli. Organism_taxid: 562. (4)

1a	1f4mD00	D:1-57
1b	1f4mF00	F:4-57
1c	1f4mE00	E:5-57
1d	1f4mA00	A:1-56
1e	1f4mB00	B:2-57
1f	1f4mC00	C:2-55

(no "Pfam Domain" information available for 1F4M)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (ROP_ECOLX | P03051)

biological process
	GO:0006355		regulation of transcription, DNA-templated		Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351		transcription, DNA-templated		The cellular synthesis of RNA on a template of DNA.

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Biological Units
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1b6q	X-RAY STRUCTURE OF A31P ROP MUTANT
1f4n	X-RAY STRUCTURE OF ALA2ILE2-6 IN THE C2 CRYSTAL FORM
1gto	X-RAY STRUCTURE OF D30G ROP MUTANT
1nkd	ATOMIC RESOLUTION X-RAY STRUCTURE OF ROP MUTANT <2AA>
1rop	X-RAY STRUCTURE OF ROP
1rpo	X-RAY STRUCTURE OF ROP MUTANT WITH ALA INSERTED ON EITHER SIDE OF ASP31
1rpr	NMR STRUCTURE OF ROP

Description

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Ligands, Modified Residues, Ions (1, 6)

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