5HQM - JenaLib

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   STRUCTURE FUNCTION STUDIES OF R. PALUSTRIS RUBISCO (R. PALUSTRIS/R. RUBRUM CHIMERA)

Authors :   M. A. Arbing, A. Shin, D. Cascio, S. Satagopan, F. R. Tabita

Date :   21 Jan 16 (Deposition) - 25 Jan 17 (Release) - 25 Jan 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Rubisco, Hexamer, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Arbing, S. Satagopan, V. A. Varaljay, F. R. Tabita
Structure Function Studies Of R. Palustris Rubisco.
To Be Published
PubMed: search

Molecule 1 - RIBULOSE BISPHOSPHATE CARBOXYLASE (R. PALUSTRIS/R. RUBRUM CHIMERA),RIBULOSE BISPHOSPHATE CARBOXYLASE
	Chains	:	A, B
	EC Number	:	4.1.1.39
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CBBM, CBBL2, RBPL
	Organism Scientific	:	RHODOPSEUDOMONAS PALUSTRIS, RHODOSPIRILLUM RUBRUM
	Organism Taxid	:	1076, 1085
	Synonym	:	RUBISCO

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	CAP	2	Ligand/Ion	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
2	K	2	Ligand/Ion	POTASSIUM ION
3	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
4	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	CAP	6	Ligand/Ion	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
2	K	-1	Ligand/Ion	POTASSIUM ION
3	KCX	6	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:165 , LYS A:167 , LYS A:169 , KCX A:192 , ASP A:194 , GLU A:195 , HIS A:288 , ARG A:289 , HIS A:322 , LYS A:330 , MET A:331 , SER A:369 , GLY A:370 , GLY A:371 , GLY A:394 , GLY A:395 , MG A:502 , HOH A:614 , HOH A:617 , HOH A:644 , HOH A:666 , HOH A:681 , HOH A:687 , HOH A:688 , GLU B:49 , THR B:54 , ASN B:112 , HOH B:626	binding site for residue CAP A 501
2	AC2	SOFTWARE	LYS A:169 , KCX A:192 , ASP A:194 , GLU A:195 , CAP A:501 , ASN B:112	binding site for residue MG A 502
3	AC3	SOFTWARE	LEU A:10 , LEU A:12 , TYR A:73	binding site for residue K A 503
4	AC4	SOFTWARE	THR A:54 , ASN A:112 , ILE B:165 , LYS B:167 , LYS B:169 , KCX B:192 , ASP B:194 , GLU B:195 , HIS B:288 , ARG B:289 , HIS B:322 , LYS B:330 , MET B:331 , SER B:369 , GLY B:370 , GLY B:371 , GLY B:394 , GLY B:395 , MG B:502 , HOH B:604 , HOH B:615 , HOH B:623 , HOH B:697	binding site for residue CAP B 501
5	AC5	SOFTWARE	ASN A:112 , KCX B:192 , ASP B:194 , GLU B:195 , CAP B:501	binding site for residue MG B 502
6	AC6	SOFTWARE	LEU B:10 , LEU B:12 , TYR B:73 , HOH B:718	binding site for residue K B 503

(no "SS Bond" information available for 5HQM)

Asymmetric Unit

No.	Residues
1	Lys A:167	-	Pro A:168
2	Lys B:167	-	Pro B:168

(no "SAP(SNP)/Variant" information available for 5HQM)

(no "PROSITE Motif" information available for 5HQM)

(no "Exon" information available for 5HQM)

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:459
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhh.eeeeeeeeee.....hhhhhhhhhhhhh...........hhhhhh...eeeeeehhh.eeeeeee.hhh.........hhhhhhhhhhhhhhhh..eeeeeeeeee.hhhhhh.......hhhhhhhhhh........eeeee.......hhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhh...eeeee...hhhhhh.....eehhhhhhhhhhhhh..eee...........hhhhhhhhhhhhh.eee....eee.......eeeee......hhhhhhhhhh....eee.hhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hqm A   3 QSNRYANLNLKESELIAGGRHVLCAYIMKPKAGFGNFIQTAAHFAAESSTGTNVEVSTTDDFTRGVDALVYEVDEANSLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIkNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFADNADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKLGVEDT 461
                                    12        22        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       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452         
                                                                                                                                                                                                                       192-KCX

Chain B from PDB  Type:PROTEIN  Length:454
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....hhhhhhhhh.eeeeeeeeee.....hhhhhhhhhhhhh...........hhhhhh...eeeeeehhh.eeeeeee.hhh.........hhhhhhhhhhhhhhh...eeeeeeeeee.hhhhhh.......hhhhhhhhhh........eeeee.......hhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhh...eeeee...hhhhhh.....eehhhhhhhhhhhhh..eee...........hhhhhhhhhhhhh.eee....eee.......eeeee......hhhhhhhhhh....eee.hhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhh.hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hqm B   1 MDQSNRYANLNLKESELIAGGRHVLCAYIMKPKAGFGNFIQTAAHFAAESSTGTNVEVSTTDDFTRGVDALVYEVDEANSLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIkNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFADNADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRA 454
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 |     200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450    
                                                                                                                                                                                                                         192-KCX

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 5HQM)

(no "CATH Domain" information available for 5HQM)

(no "Pfam Domain" information available for 5HQM)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		CAP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		K	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		KCX	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Lys A:167 - Pro A:168	[ RasMol ]
		Lys B:167 - Pro B:168	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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