Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF AROMATIC MUTANT (F4W) OF AN ALKALI THERMOSTABLE GH10 XYLANASE FROM BACILLUS SP. NG-27
 
Authors :  P. Mahanta, A. Bhardwaj, V. S. Reddy, S. Ramakumar
Date :  18 Oct 15  (Deposition) - 19 Oct 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glycosyl Hydrolase Famility 10, Xylanase, (Beta/Alpha)8-Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Mahanta, A. Bhardwaj, V. S. Reddy, S. Ramakumar
Crystal Structure Of Aromatic Mutant (F4W) Of An Alkali Thermostable Gh10 Xylanase From Bacillus Sp. Ng-27
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BETA-XYLANASE
    Chains: A, B
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Strain: BL21-GOLD(DE3)PLYSS AG
    Expression System Taxid: 866768
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 52-405
    Mutation: YES
    Organism Scientific: BACILLUS SP. NG-27
    Organism Taxid: 65673
    Synonym: ALKALI THERMOSTABLE GH10 ENDOXYLANASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2NA2Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NA-1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:292 , ARG A:351 , ASP A:354 , HOH A:504 , HOH A:558 , HOH A:564 , HOH A:652binding site for residue MG A 401
2AC2SOFTWARESER A:18 , ASP A:302 , LEU A:305 , HOH A:702 , HOH A:724binding site for residue NA A 402
3AC3SOFTWAREASN B:292 , ARG B:351 , ASP B:354 , HOH B:553 , HOH B:560 , HOH B:593 , HOH B:599binding site for residue MG B 401
4AC4SOFTWARESER B:18 , ASP B:302 , LEU B:305 , HOH B:639 , HOH B:650binding site for residue NA B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EB8)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1His A:85 -Thr A:86
2Thr A:202 -Pro A:203
3Trp A:235 -Pro A:236
4Trp A:267 -Pro A:268
5Arg A:270 -Pro A:271
6His B:85 -Thr B:86
7Thr B:202 -Pro B:203
8Trp B:235 -Pro B:236
9Trp B:267 -Pro B:268
10Arg B:270 -Pro B:271

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EB8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EB8)

(-) Exons   (0, 0)

(no "Exon" information available for 5EB8)

(-) 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:354
                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh.hhhhhh....eeeeeehhhhhhhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeeee........hhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee...............hhhhhhhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhh.....eeee..ee.....hhhhhhhhhhhhhhh..eeeeeeeee.................hhhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhh..................hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5eb8 A   1 VQPWAWQVASLADRYEESFDIGAAVEPHQLNGRQGKVLKHHYNSIVAENAMKPISLQPEEGVFTWDGADAIVEFARKNNMNLRFHTLVWHNQVPDWFFLDEEGNPMVEETNEAKRQANKELLLERLETHIKTVVERYKDDVTAWDVVNEVVDDGTPNERGLRESVWYQITGDEYIRVAFETARKYAGEDAKLFINDYNTEVTPKRDHLYNLVQDLLADGVPIDGVGHQAHIQIDWPTIDEIRTSMEMFAGLGLDNQVTELDVSLYGWPPRPAFPTYDAIPQERFQAQADRYNQLFELYEELDADLSSVTFWGIADNHTWLDDRAREYNDGVGKDAPFVFDPNYRVKPAFWRIID 354
                                    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    


Chain B from PDB  Type:PROTEIN  Length:354
                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh.hhhhhh....eeeeeehhhhhhhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeeee........hhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee...............hhhhhhhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhh.....eeee..ee.....hhhhhhhhhhhhhhh..eeeeeeeee.................hhhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhh..................hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5eb8 B   1 VQPWAWQVASLADRYEESFDIGAAVEPHQLNGRQGKVLKHHYNSIVAENAMKPISLQPEEGVFTWDGADAIVEFARKNNMNLRFHTLVWHNQVPDWFFLDEEGNPMVEETNEAKRQANKELLLERLETHIKTVVERYKDDVTAWDVVNEVVDDGTPNERGLRESVWYQITGDEYIRVAFETARKYAGEDAKLFINDYNTEVTPKRDHLYNLVQDLLADGVPIDGVGHQAHIQIDWPTIDEIRTSMEMFAGLGLDNQVTELDVSLYGWPPRPAFPTYDAIPQERFQAQADRYNQLFELYEELDADLSSVTFWGIADNHTWLDDRAREYNDGVGKDAPFVFDPNYRVKPAFWRIID 354
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 5EB8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EB8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EB8)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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
    Arg A:270 - Pro A:271   [ RasMol ]  
    Arg B:270 - Pro B:271   [ RasMol ]  
    His A:85 - Thr A:86   [ RasMol ]  
    His B:85 - Thr B:86   [ RasMol ]  
    Thr A:202 - Pro A:203   [ RasMol ]  
    Thr B:202 - Pro B:203   [ RasMol ]  
    Trp A:235 - Pro A:236   [ RasMol ]  
    Trp A:267 - Pro A:268   [ RasMol ]  
    Trp B:235 - Pro B:236   [ RasMol ]  
    Trp B:267 - Pro B:268   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  5eb8
    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
  O30700_9BACI | O30700
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.2.1.8
    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
  O30700_9BACI | O30700
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        O30700_9BACI | O30700: 2f8q 2fgl 4qce 4qcf 4qdm 5eba 5efd 5eff

(-) Related Entries Specified in the PDB File

5eba