3CZ5 - JenaLib

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Title :   CRYSTAL STRUCTURE OF TWO-COMPONENT RESPONSE REGULATOR, LUXR FAMILY, FROM AURANTIMONAS SP. SI85-9A1

Authors :   V. N. Malashkevich, R. Toro, S. R. Wasserman, A. Meyer, J. M. Sauder, S. K S. C. Almo, New York Sgx Research Center For Structural Genomi (Nysgxrc)

Date :   28 Apr 08 (Deposition) - 06 May 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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 :   Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Response Regulator, Luxr Family, Psi-2, Dna-Binding, Transcription, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. N. Malashkevich, R. Toro, S. R. Wasserman, A. Meyer, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Two-Component Response Regulator, Luxr Family, From Aurantimonas Sp. Si85-9A1.
To Be Published
PubMed: search

Molecule 1 - TWO-COMPONENT RESPONSE REGULATOR, LUXR FAMILY
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BC-PSGX3(BC)
	Expression System Strain	:	BL21(DE3)CODON+RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 2-143
	Gene	:	SI859A1_03491
	Organism Scientific	:	AURANTIMONAS SP.
	Organism Taxid	:	314269
	Strain	:	SI85-9A1

		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 (1, 4)

No.	Name	Count	Type	Full Name
1	PO4	4	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	PO4	-1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:58 , LEU A:59 , THR A:60 , THR A:86 , MET A:87 , LYS A:108 , HOH A:209 , HOH A:210	BINDING SITE FOR RESIDUE PO4 A 201
2	AC2	SOFTWARE	HIS A:14 , PRO A:15 , ILE A:16 , VAL A:17 , GLU B:49 , ARG C:23 , ARG C:27	BINDING SITE FOR RESIDUE PO4 A 202
3	AC3	SOFTWARE	HIS B:14 , ASP B:58 , LEU B:59 , THR B:60 , THR B:86 , MET B:87 , LYS B:108 , HOH B:215	BINDING SITE FOR RESIDUE PO4 B 201
4	AC4	SOFTWARE	ASP C:58 , LEU C:59 , THR C:60 , PHE C:85 , THR C:86 , MET C:87 , LYS C:108	BINDING SITE FOR RESIDUE PO4 C 201

(no "SS Bond" information available for 3CZ5)

(no "Cis Peptide Bond" information available for 3CZ5)

(no "SAP(SNP)/Variant" information available for 3CZ5)

(no "PROSITE Motif" information available for 3CZ5)

(no "Exon" information available for 3CZ5)

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:141
 aligned with Q1YEP2_AURMS | Q1YEP2 from UniProtKB/TrEMBL  Length:212

    Alignment length:141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 
         Q1YEP2_AURMS     2 STARIMLVDDHPIVREGYRRLIERRPGYAVVAEAADAGEAYRLYRETTPDIVVMDLTLPGPGGIEATRHIRQWDGAARILIFTMHQGSAFALKAFEAGASGYVTKSSDPAELVQAIEAILAGRRAMSPDIAQEIAEERVEG 142
               SCOP domains d3cz5a_ A: automated matches                                                                                                                  SCOP domains
               CATH domains 3cz5A00 A:4-144  [code=3.40.50.2300, no name defined]                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhh....eeee.......hhhhhhhhhhhhh....eeeee...hhhhhhhhhhh...eeee.....hhhhhhhhhhh....eehhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cz5 A   4 STARIMLVDDHPIVREGYRRLIERRPGYAVVAEAADAGEAYRLYRETTPDIVVMDLTLPGPGGIEATRHIRQWDGAARILIFTMHQGSAFALKAFEAGASGYVTKSSDPAELVQAIEAILAGRRAMSPDIAQEIAEERVEG 144
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143

Chain B from PDB  Type:PROTEIN  Length:140
 aligned with Q1YEP2_AURMS | Q1YEP2 from UniProtKB/TrEMBL  Length:212

    Alignment length:140
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141
         Q1YEP2_AURMS     2 STARIMLVDDHPIVREGYRRLIERRPGYAVVAEAADAGEAYRLYRETTPDIVVMDLTLPGPGGIEATRHIRQWDGAARILIFTMHQGSAFALKAFEAGASGYVTKSSDPAELVQAIEAILAGRRAMSPDIAQEIAEERVE 141
               SCOP domains d3cz5b_ B: automated matches                                                                                                                 SCOP domains
               CATH domains 3cz5B00 B:4-143  [code=3.40.50.2300, no name defined]                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh..eeee.....hhhhhhhhhhhh...eehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cz5 B   4 STARIMLVDDHPIVREGYRRLIERRPGYAVVAEAADAGEAYRLYRETTPDIVVMDLTLPGPGGIEATRHIRQWDGAARILIFTMHQGSAFALKAFEAGASGYVTKSSDPAELVQAIEAILAGRRAMSPDIAQEIAEERVE 143
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143

Chain C from PDB  Type:PROTEIN  Length:142
 aligned with Q1YEP2_AURMS | Q1YEP2 from UniProtKB/TrEMBL  Length:212

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
         Q1YEP2_AURMS     2 STARIMLVDDHPIVREGYRRLIERRPGYAVVAEAADAGEAYRLYRETTPDIVVMDLTLPGPGGIEATRHIRQWDGAARILIFTMHQGSAFALKAFEAGASGYVTKSSDPAELVQAIEAILAGRRAMSPDIAQEIAEERVEGR 143
               SCOP domains d3cz5c_ C: automated matches                                                                                                                   SCOP domains
               CATH domains 3cz5C00 C:4-145  [code=3.40.50.2300, no name defined]                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh....eeeee...hhhhhhhhhhh...eeee....hhhhhhhhhhhhhh..eehhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cz5 C   4 STARIMLVDDHPIVREGYRRLIERRPGYAVVAEAADAGEAYRLYRETTPDIVVMDLTLPGPGGIEATRHIRQWDGAARILIFTMHQGSAFALKAFEAGASGYVTKSSDPAELVQAIEAILAGRRAMSPDIAQEIAEERVEGR 145
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143

Chain D from PDB  Type:PROTEIN  Length:142
 aligned with Q1YEP2_AURMS | Q1YEP2 from UniProtKB/TrEMBL  Length:212

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
         Q1YEP2_AURMS     2 STARIMLVDDHPIVREGYRRLIERRPGYAVVAEAADAGEAYRLYRETTPDIVVMDLTLPGPGGIEATRHIRQWDGAARILIFTMHQGSAFALKAFEAGASGYVTKSSDPAELVQAIEAILAGRRAMSPDIAQEIAEERVEGR 143
               SCOP domains d3cz5d_ D: automated matches                                                                                                                   SCOP domains
               CATH domains 3cz5D00 D:4-145  [code=3.40.50.2300, no name defined]                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.......hhhhhhhhhh...eeeeee.hhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cz5 D   4 STARIMLVDDHPIVREGYRRLIERRPGYAVVAEAADAGEAYRLYRETTPDIVVMDLTLPGPGGIEATRHIRQWDGAARILIFTMHQGSAFALKAFEAGASGYVTKSSDPAELVQAIEAILAGRRAMSPDIAQEIAEERVEGR 145
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Flavodoxin-like (1057)

Superfamily: CheY-like (258)

Family: automated matches (82)

Protein domain: automated matches (82)

Aurantimonas sp. [TaxId: 314269] (1)

1a	d3cz5a_	A:
1b	d3cz5b_	B:
1c	d3cz5c_	C:
1d	d3cz5d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.2300, no name defined] (308)

Si85-9a1 (Aurantimonas sp) (1)

1a	3cz5B00	B:4-143
1b	3cz5A00	A:4-144
1c	3cz5C00	C:4-145
1d	3cz5D00	D:4-145

(no "Pfam Domain" information available for 3CZ5)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q1YEP2_AURMS | Q1YEP2)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
	GO:0000160	phosphorelay signal transduction system	A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
	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.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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