3FM5 - JenaLib

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Title :   X-RAY CRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR (MARR FAMILY) FROM RHODOCOCCUS SP. RHA1

Authors :   B. Nocek, X. Xu, H. Zheng, A. Savchenko, A. M. Edwards, A. Joachimiak, Mi Center For Structural Genomics (Mcsg)

Date :   19 Dec 08 (Deposition) - 03 Feb 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Transcriptional Regulator, Mcsg, Pf04017, Psi, Marr, Structural Genomics, Protein Structure Initiative, Midwest Center For Structural Genomics, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Nocek, X. Xu, H. Zheng, A. Savchenko, A. M. Edwards, A. Joachimiak
X-Ray Crystal Structure Of Transcriptional Regulator (Marr Family) From Rhodococcus Sp. Rha1
To Be Published
PubMed: search

Molecule 1 - TRANSCRIPTIONAL REGULATOR
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RHA1_RO05125
	Organism Scientific	:	RHODOCOCCUS JOSTII
	Organism Taxid	:	101510
	Strain	:	RHA1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 19)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	GOL	2	Ligand/Ion	GLYCEROL
4	MG	1	Ligand/Ion	MAGNESIUM ION
5	MSE	13	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	GOL	1	Ligand/Ion	GLYCEROL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	MSE	7	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (3, 9)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	GOL	1	Ligand/Ion	GLYCEROL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (3, 17)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	GOL	2	Ligand/Ion	GLYCEROL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	MSE	13	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:65 , SER A:67 , GLN A:68 , ARG D:17	BINDING SITE FOR RESIDUE GOL A 303
2	AC2	SOFTWARE	PHE B:121 , GLY B:123 , ILE B:124 , ASP B:126 , HOH B:155 , HOH B:201	BINDING SITE FOR RESIDUE EDO B 302
3	AC3	SOFTWARE	ASP C:134 , GLN C:137 , HOH C:200 , HOH C:202 , HOH C:219 , HOH C:300	BINDING SITE FOR RESIDUE MG C 201
4	AC4	SOFTWARE	LEU B:23 , SER B:41 , MSE B:62 , SER D:16 , ARG D:17 , HOH D:184 , HOH D:189	BINDING SITE FOR RESIDUE GOL D2001
5	AC5	SOFTWARE	GLN D:55 , ARG D:84	BINDING SITE FOR RESIDUE CL D 202
6	AC6	SOFTWARE	LEU D:23 , ASN D:27 , ARG D:36 , VAL D:37 , ARG D:38 , HOH D:170	BINDING SITE FOR RESIDUE EDO D 301

(no "SS Bond" information available for 3FM5)

(no "Cis Peptide Bond" information available for 3FM5)

(no "SAP(SNP)/Variant" information available for 3FM5)

(no "PROSITE Motif" information available for 3FM5)

(no "Exon" information available for 3FM5)

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:131
 aligned with Q0S6D0_RHOJR | Q0S6D0 from UniProtKB/TrEMBL  Length:146

    Alignment length:142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  
         Q0S6D0_RHOJR     1 MAESQALSDDIGFLLSRVGGMVLGAVNKALVPTGLRVRSYSVLVLACEQAEGVNQRGVAATMGLDPSQIVGLVDELEERGLVVRTLDPSDRRNKLIAATEEGRRLRDDAKARVDAAHGRYFEGIPDTVVNQMRDTLQSIAFP 142
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3fm5A00 A:2-142 'winged helix' repressor DNA binding domain                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhh.hhhhhhhhhhhhhh...ee.-----------.eehhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fm5 A   1 mAESQALSDDIGFLLSRVGGmVLGAVNKALVPTGLRVRSYSVLVLACEQAEGVNQRGVAATmGLDPSQIVGLVDELEERGLVVR-----------IAATEEGRRLRDDAKARVDAAHGRYFEGIPDTVVNQmRDTLQSIAFP 142
                            |       10        20|       30        40        50        60 |      70        80   |     -     | 100       110       120       130 |     140  
                            |                  21-MSE                                   62-MSE                84          96                                 132-MSE      
                            1-MSE

Chain B from PDB  Type:PROTEIN  Length:140
 aligned with Q0S6D0_RHOJR | Q0S6D0 from UniProtKB/TrEMBL  Length:146

    Alignment length:142
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143  
         Q0S6D0_RHOJR     4 SQALSDDIGFLLSRVGGMVLGAVNKALVPTGLRVRSYSVLVLACEQAEGVNQRGVAATMGLDPSQIVGLVDELEERGLVVRTLDPSDRRNKLIAATEEGRRLRDDAKARVDAAHGRYFEGIPDTVVNQMRDTLQSIAFPTFV 145
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fm5B00 B:4-145 'winged helix' repressor DNA binding domain                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....eehhhhhhhhh.hhhhhhhhhhhhhhh..eeeee..--...eeeeehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fm5 B   4 SQALSDDIGFLLSRVGGmVLGAVNKALVPTGLRVRSYSVLVLACEQAEGVNQRGVAATmGLDPSQIVGLVDELEERGLVVRTLDP--RRNKLIAATEEGRRLRDDAKARVDAAHGRYFEGIPDTVVNQmRDTLQSIAFPTFV 145
                                    13       |23        33        43        53        63        73        83    |  |93       103       113       123       133       143  
                                            21-MSE                                   62-MSE                    88 91                                      132-MSE

Chain C from PDB  Type:PROTEIN  Length:137
 aligned with Q0S6D0_RHOJR | Q0S6D0 from UniProtKB/TrEMBL  Length:146

    Alignment length:140
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143
         Q0S6D0_RHOJR     4 SQALSDDIGFLLSRVGGMVLGAVNKALVPTGLRVRSYSVLVLACEQAEGVNQRGVAATMGLDPSQIVGLVDELEERGLVVRTLDPSDRRNKLIAATEEGRRLRDDAKARVDAAHGRYFEGIPDTVVNQMRDTLQSIAFPT 143
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fm5C00 C:4-143 'winged helix' repressor DNA binding domain                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...eehhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee.---.eeeeeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fm5 C   4 SQALSDDIGFLLSRVGGmVLGAVNKALVPTGLRVRSYSVLVLACEQAEGVNQRGVAATmGLDPSQIVGLVDELEERGLVVRTLDP---RNKLIAATEEGRRLRDDAKARVDAAHGRYFEGIPDTVVNQmRDTLQSIAFPT 143
                                    13       |23        33        43        53        63        73        83    |   93       103       113       123       133       143
                                            21-MSE                                   62-MSE                    88  92                                     132-MSE

Chain D from PDB  Type:PROTEIN  Length:138
 aligned with Q0S6D0_RHOJR | Q0S6D0 from UniProtKB/TrEMBL  Length:146

    Alignment length:140
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143
         Q0S6D0_RHOJR     4 SQALSDDIGFLLSRVGGMVLGAVNKALVPTGLRVRSYSVLVLACEQAEGVNQRGVAATMGLDPSQIVGLVDELEERGLVVRTLDPSDRRNKLIAATEEGRRLRDDAKARVDAAHGRYFEGIPDTVVNQMRDTLQSIAFPT 143
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fm5D00 D:4-143 'winged helix' repressor DNA binding domain                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....eehhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee..e--eeeeeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fm5 D   4 SQALSDDIGFLLSRVGGmVLGAVNKALVPTGLRVRSYSVLVLACEQAEGVNQRGVAATmGLDPSQIVGLVDELEERGLVVRTLDPSD--NKLIAATEEGRRLRDDAKARVDAAHGRYFEGIPDTVVNQmRDTLQSIAFPT 143
                                    13       |23        33        43        53        63        73        83      | 93       103       113       123       133       143
                                            21-MSE                                   62-MSE                      90 93                                    132-MSE

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 '\|'

(no "SCOP Domain" information available for 3FM5)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

Rhodococcus jostii rha1. Organism_taxid: 101510. Strain: rha1. (1)

1a	3fm5A00	A:2-142
1b	3fm5C00	C:4-143
1c	3fm5D00	D:4-143
1d	3fm5B00	B:4-145

(no "Pfam Domain" information available for 3FM5)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q0S6D0_RHOJR | Q0S6D0)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
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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	Cis Peptide Bonds
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Description

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Ligands, Modified Residues, Ions (5, 19)

Sites (6, 6)

SS Bonds (0, 0)

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