4GYO - JenaLib

Title :   CRYSTAL STRUCTURE OF RAP PROTEIN COMPLEXED WITH COMPETENCE AND SPORULATION FACTOR

Authors :   V. Parashar, M. B. Neiditch

Date :   05 Sep 12 (Deposition) - 03 Apr 13 (Release) - 10 Apr 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.16

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

Keywords :   Tetratricopeptide Repeat, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Parashar, P. D. Jeffrey, M. B. Neiditch
Conformational Change-Induced Repeat Domain Expansion Regulates Rap Phosphatase Quorum-Sensing Signal Receptors.
Plos Biol. V. 11 01512 2013
PubMed-ID: 23526881 | Reference-DOI: 10.1371/JOURNAL.PBIO.1001512

Compounds

Molecule 1 - RESPONSE REGULATOR ASPARTATE PHOSPHATASE J
	Chains	:	A, B
	EC Number	:	3.1.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	BSU02820, RAPJ, YCDE
	Organism Scientific	:	BACILLUS SUBTILIS SUBSP. SUBTILIS
	Organism Taxid	:	224308
	Strain	:	168

Molecule 2 - CSF PEPTIDE
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	SYNTHETICALLY PRODUCED MATURE PEPTIDE CSF
	Synthetic	:	YES

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 2)

Asymmetric Unit (1, 2)

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

Biological Unit 1 (0, 0)

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

Biological Unit 2 (0, 0)

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

Biological Unit 3 (0, 0)

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

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:177 , ARG A:178 , HOH A:503	BINDING SITE FOR RESIDUE CL A 401
2	AC2	SOFTWARE	ARG B:177 , ARG B:178 , HOH B:544	BINDING SITE FOR RESIDUE CL B 401

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:357
                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gyo A   6 PSEEVAVKLNEWYKLIRAFEADQAEALKQEIEYDLEDMEENQDLLLYFSLMEFRHRIMLDKLMPVKPFSDMLNEIESNLTGLLEYYFYYFRGMYEFKQKNFILAIDHYKHAEEKLEYVEDEIEKAEFLFKVAEVYYHIKQTYFSMNYASQALDIYTKYELYGRRRVQCEFIIAGNLTDVYHHEKALTHLCSALEHARQLEEAYMIAAAYYNVGHCKYSLGDYKEAEGYFKTAAAIFEEHNFQQAVQAVFSLTHIYCKEGKYDKAVEAYDRGIKSAAEWEDDMYLTKFRLIHELYLGSGDLNVLTECFDLLESRQLLADAEDLLHDTAERFNQLEHYESAAFFYRRLMNIKKKLAEQR 371
                                    15        25        35        45        55        65     || 81       |94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       
                                                                                            71|         89|                                                                                                                                                                                                                                                                                      
                                                                                             78          93

Chain B from PDB  Type:PROTEIN  Length:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gyo B   7 SEEVAVKLNEWYKLIRAFEADQAEALKQEIEYDLEDMEENQDLLLYFSLMEFRHRIMLDKLMPVKPFSDMLNEIESNQQKLTGLLEYYFYYFRGMYEFKQKNFILAIDHYKHAEEKLEYVEDEIEKAEFLFKVAEVYYHIKQTYFSMNYASQALDIYTKYELYGRRRVQCEFIIAGNLTDVYHHEKALTHLCSALEHARQLEEAYMIAAAYYNVGHCKYSLGDYKEAEGYFKTAAAIFEEHNFQQAVQAVFSLTHIYCKEGKYDKAVEAYDRGIKSAAEWEDDMYLTKFRLIHELYLGSGDLNVLTECFDLLESRQLLADAEDLLHDTAERFNQLEHYESAAFFYRRLMNIKKKLAEQR 371
                                    16        26        36        46        56        66    ||  82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362         
                                                                                           71|                                                                                                                                                                                                                                                                                                     
                                                                                            78

Chain C from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4gyo C   1 ERGMT   5

Chain D from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4gyo D   1 ERGMT   5

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (3, 3)

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	Cis Peptide Bonds
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Biological Units
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Description