2QMT - JenaLib

Title :   CRYSTAL POLYMORPHISM OF PROTEIN GB1 EXAMINED BY SOLID-STATE NMR AND X-RAY DIFFRACTION

Authors :   H. L. Frericks Schmidt, L. J. Sperling, Y. G. Gao, B. J. Wylie, J. M. Boettcher, S. R. Wilson, C. M. Rienstra

Date :   16 Jul 07 (Deposition) - 25 Dec 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.05

Chains :   Asym./Biol. Unit : A

Keywords :   Immunglobulin Binding Domain, Thermostable, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. L. Frericks Schmidt, L. J. Sperling, Y. G. Gao, B. J. Wylie, J. M. Boettcher, S. R. Wilson, C. M. Rienstra
Crystal Polymorphism Of Protein Gb1 Examined By Solid-State Nmr Spectroscopy And X-Ray Diffraction.
J. Phys. Chem. B V. 111 14362 2007
PubMed-ID: 18052145 | Reference-DOI: 10.1021/JP075531P
(for further references see the PDB file header)

Compounds

Molecule 1 - IMMUNOGLOBULIN G-BINDING PROTEIN G
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	IMMUNOGLOBULIN BETA 1 BINDING DOMAIN (RESIDUES 303-357)
	Gene	:	SPG
	Mutation	:	YES
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Other Details	:	SYNTHESIZED PLASMID, PREPARED ACCORDING TO SMITH, C., WITHKA, J., AND REGAN, L. BIOCHEMISTRY 1994, 33, 5510-5517, EXPRESSING PROTEIN IDENTICAL IN SEQUENCE AND STRUCTURE TO THE IGG BETA 1 BINDING DOMAIN OF PROTEIN G OF STREPTOCOCCUS AREUS
	Synonym	:	IGG-BINDING PROTEIN G

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:3 , ASP A:22 , ALA A:23 , ASP A:47 , LYS A:50 , HOH A:1058 , HOH A:1073 , HOH A:1077	BINDING SITE FOR RESIDUE PO4 A 101
2	AC2	SOFTWARE	ALA A:20 , VAL A:21 , GLU A:27 , LYS A:31 , TRP A:43 , HOH A:1021 , HOH A:1089	BINDING SITE FOR RESIDUE MRD A 102
3	AC3	SOFTWARE	ALA A:24 , GLU A:27 , TYR A:45 , PHE A:52 , HOH A:1030	BINDING SITE FOR RESIDUE IPA A 203
4	AC4	SOFTWARE	ASN A:8 , THR A:55 , HOH A:1094 , HOH A:1147	BINDING SITE FOR RESIDUE IPA A 204

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/Biological 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 SPG2_STRSG | P19909 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:56
                                   311       321       331       341       351      
           SPG2_STRSG   302 DTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE 357
               SCOP domains d2qmta_ A:                                               SCOP domains
               CATH domains 2qmtA00 A:1-56  [code=3.10.20.10, no name defined]       CATH domains
               Pfam domains --IgG_binding_B-2qmtA01 A:3-56                           Pfam domains
         Sec.struct. author .eeeeeee....eeeeeee..hhhhhhhhhhhhhhhh....eeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 2qmt A   1 MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE  56
                                    10        20        30        40        50

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SPG2_STRSG | P19909)

molecular function
	GO:0019864	IgG binding	Interacting selectively and non-covalently with an immunoglobulin of an IgG isotype.
biological process
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
	GO:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		IPA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MRD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2qmt)

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2qmt
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	SPG2_STRSG \| P19909
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	SPG2_STRSG \| P19909
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

1pga	ALTERNATIVE ORTHORHOMBIC SINGLE CRYSTAL STRUCTURE OF GB1
1pgb	ALTERNATIVE TRIGONAL SINGLE CRYSTAL STRUCTURE OF GB1
2gb1	AVERAGE SOLUTION NMR STRUCTURE OF GB1
2gi9	ORTHORHOMBIC SINGLE CRYSTAL STRUCTURE OF GB1 - 1.14 RESOLUTION RELATED ID: 15156 RELATED DB: BMRB SOLID-STATE NMR CHEMICAL SHIFT ASSIGNMENTS OF GB1
2jsv	ENSEMBLE OF SOLID-STATE NMR STRUCTURES OF GB1

Description