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(-) Description

Title :  CRYSTAL STRUCTURE OF RPIA-R5P COMPLEX
 
Authors :  R. Rostankowski, D. Borek, M. Orlikowska, C. Nakka, S. Grimshaw, Z. Otw Center For Structural Genomics Of Infectious Diseases (Csgi
Date :  13 Aug 13  (Deposition) - 02 Oct 13  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.37
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Rostankowski, D. Borek, M. Orlikowska, C. Nakka, S. Grimshaw, Z. Otwinowski, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Rpia-R5P Complex
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBOSE-5-PHOSPHATE ISOMERASE A
    Chains: A, B, C, D
    EC Number: 5.3.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 866768
    Expression System Vector Type: PLASMID
    Gene: RPIA, FTW_1255
    Organism Scientific: FRANCISELLA TULARENSIS
    Organism Taxid: 263
    Synonym: PHOSPHORIBOISOMERASE A, PRI

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 50)

Asymmetric Unit (3, 50)
No.NameCountTypeFull Name
15RP4Ligand/IonRIBULOSE-5-PHOSPHATE
2ARF41Ligand/IonFORMAMIDE
3CL5Ligand/IonCHLORIDE ION
Biological Unit 1 (2, 28)
No.NameCountTypeFull Name
15RP2Ligand/IonRIBULOSE-5-PHOSPHATE
2ARF26Ligand/IonFORMAMIDE
3CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (2, 17)
No.NameCountTypeFull Name
15RP2Ligand/IonRIBULOSE-5-PHOSPHATE
2ARF15Ligand/IonFORMAMIDE
3CL-1Ligand/IonCHLORIDE ION

(-) Sites  (47, 47)

Asymmetric Unit (47, 47)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:34 , GLY A:35 , SER A:36 , THR A:37 , ASP A:87 , GLY A:88 , ALA A:89 , ASP A:90 , LYS A:100 , GLY A:101 , GLY A:102 , GLY A:103 , ALA A:104 , ALA A:105 , GLU A:109 , LYS A:127 , HOH A:425 , HOH A:457 , HOH A:469BINDING SITE FOR RESIDUE 5RP A 301
02AC2SOFTWAREVAL A:113 , GLU A:189 , PHE A:204 , LYS A:207 , HOH A:407 , HOH A:480BINDING SITE FOR RESIDUE ARF A 302
03AC3SOFTWAREHIS A:95 , ASP A:183 , HOH A:492BINDING SITE FOR RESIDUE ARF A 303
04AC4SOFTWARELYS A:67 , PHE A:71 , ASP A:72BINDING SITE FOR RESIDUE ARF A 304
05AC5SOFTWAREHIS A:95 , GLU A:97BINDING SITE FOR RESIDUE ARF A 305
06AC6SOFTWAREASP A:61 , GLY A:103 , HOH A:489BINDING SITE FOR RESIDUE ARF A 307
07AC7SOFTWARESER A:36 , GLY A:39 , PHE A:40 , LYS A:65 , HOH A:427 , HOH A:432 , HOH A:496BINDING SITE FOR RESIDUE ARF A 308
08AC8SOFTWAREHOH A:420 , HOH A:421BINDING SITE FOR RESIDUE ARF A 309
09AC9SOFTWAREASN A:94 , HIS A:95 , LYS A:96BINDING SITE FOR RESIDUE ARF A 311
10BC1SOFTWAREGLU A:189 , ASN A:193 , HOH A:480 , GLN C:194 , THR C:196BINDING SITE FOR RESIDUE ARF A 312
11BC2SOFTWARELYS A:67 , ASP A:72 , VAL A:73BINDING SITE FOR RESIDUE ARF A 313
12BC3SOFTWAREHOH A:433BINDING SITE FOR RESIDUE ARF A 314
13BC4SOFTWAREARG A:64 , LYS A:67 , ALA A:68 , LEU A:206BINDING SITE FOR RESIDUE ARF A 315
14BC5SOFTWAREILE A:52 , LYS A:53 , PHE A:71 , ASP A:72 , HOH A:455BINDING SITE FOR RESIDUE ARF A 316
15BC6SOFTWAREARG A:146 , GLN B:159BINDING SITE FOR RESIDUE CL A 317
16BC7SOFTWARETHR B:34 , GLY B:35 , SER B:36 , THR B:37 , ASP B:87 , GLY B:88 , ALA B:89 , ASP B:90 , LYS B:100 , GLY B:101 , GLY B:102 , GLY B:103 , ALA B:104 , ALA B:105 , GLU B:109 , LYS B:127 , HOH B:407 , HOH B:456BINDING SITE FOR RESIDUE 5RP B 301
17BC8SOFTWARETHR B:34 , GLY B:103 , HOH B:463BINDING SITE FOR RESIDUE ARF B 302
18BC9SOFTWAREHIS B:95 , LYS B:96 , ALA B:209 , HOH B:423 , HOH B:449BINDING SITE FOR RESIDUE ARF B 303
19CC1SOFTWAREALA B:68 , LYS B:207 , PRO B:208 , ASP B:210 , ARF B:308 , HOH B:405BINDING SITE FOR RESIDUE ARF B 304
20CC2SOFTWAREHIS B:95 , HOH B:426 , HOH B:474BINDING SITE FOR RESIDUE ARF B 305
21CC3SOFTWARESER B:58 , ALA B:105 , THR B:107 , ARG B:108 , ASP B:169 , ASN B:170BINDING SITE FOR RESIDUE ARF B 306
22CC4SOFTWARELYS B:67 , PHE B:71 , ASP B:72 , HOH B:459BINDING SITE FOR RESIDUE ARF B 307
23CC5SOFTWAREALA B:116 , LYS B:117 , LYS B:207 , ASP B:210 , ARF B:304BINDING SITE FOR RESIDUE ARF B 308
24CC6SOFTWAREARG B:64 , LYS B:67 , LEU B:206BINDING SITE FOR RESIDUE ARF B 309
25CC7SOFTWAREASP B:75 , ASN B:77 , HOH B:433 , HOH B:455 , PRO D:143BINDING SITE FOR RESIDUE ARF B 310
26CC8SOFTWARELYS B:110 , GLU B:189 , ASN B:193 , ARF B:313 , GLN D:194 , THR D:196BINDING SITE FOR RESIDUE ARF B 311
27CC9SOFTWAREHIS B:95 , GLU B:97BINDING SITE FOR RESIDUE ARF B 312
28DC1SOFTWAREASN B:193 , ARF B:311 , ASN D:193 , GLN D:194 , ILE D:195BINDING SITE FOR RESIDUE ARF B 313
29DC2SOFTWAREGLN A:159 , PRO A:160 , ALA B:150 , ARG B:151 , VAL B:154 , HOH B:402BINDING SITE FOR RESIDUE ARF B 314
30DC3SOFTWAREASP B:61 , ARG B:64 , ASN B:184 , LEU B:186BINDING SITE FOR RESIDUE CL B 315
31DC4SOFTWAREGLU B:164BINDING SITE FOR RESIDUE CL B 316
32DC5SOFTWAREARG B:49 , ILE B:52 , LYS B:53BINDING SITE FOR RESIDUE CL B 317
33DC6SOFTWARETHR C:34 , GLY C:35 , SER C:36 , THR C:37 , ASP C:87 , GLY C:88 , ASP C:90 , LYS C:100 , GLY C:101 , GLY C:102 , GLY C:103 , ALA C:104 , ALA C:105 , GLU C:109 , LYS C:127 , ARF C:307 , HOH C:409 , HOH C:422 , HOH C:455BINDING SITE FOR RESIDUE 5RP C 301
34DC7SOFTWARESER C:147 , ALA C:150 , ARG C:151 , VAL C:154 , ARF C:304 , HOH C:411BINDING SITE FOR RESIDUE ARF C 302
35DC8SOFTWAREMET A:144 , VAL C:56 , SER C:57 , VAL C:73 , VAL C:74 , ASP C:75 , LEU C:76 , HOH C:405BINDING SITE FOR RESIDUE ARF C 303
36DC9SOFTWAREALA C:150 , ARG C:151 , VAL C:154 , ARF C:302BINDING SITE FOR RESIDUE ARF C 304
37EC1SOFTWAREGLU C:60 , ARG C:108 , ASP C:169 , ARF C:308BINDING SITE FOR RESIDUE ARF C 306
38EC2SOFTWAREASP C:90 , PHE C:135 , 5RP C:301 , HOH C:455BINDING SITE FOR RESIDUE ARF C 307
39EC3SOFTWAREARF C:306 , ARF C:311 , HOH C:402 , HOH C:443BINDING SITE FOR RESIDUE ARF C 308
40EC4SOFTWAREPRO C:143 , GLY C:171BINDING SITE FOR RESIDUE ARF C 309
41EC5SOFTWAREGLU C:60 , ASP C:61 , GLY C:103 , ASP C:169BINDING SITE FOR RESIDUE ARF C 310
42EC6SOFTWAREHIS C:95 , GLU C:97 , ALA C:205 , PRO C:208 , ARF C:308BINDING SITE FOR RESIDUE ARF C 311
43EC7SOFTWAREARG C:163 , THR C:166 , HOH C:420BINDING SITE FOR RESIDUE ARF C 312
44EC8SOFTWAREARG C:151 , GLN C:152BINDING SITE FOR RESIDUE CL C 313
45EC9SOFTWARETHR D:34 , GLY D:35 , SER D:36 , THR D:37 , ASP D:87 , GLY D:88 , ASP D:90 , LYS D:100 , GLY D:101 , GLY D:103 , ALA D:105 , GLU D:109 , LYS D:127 , HOH D:417 , HOH D:430BINDING SITE FOR RESIDUE 5RP D 301
46FC1SOFTWARELYS D:110 , GLU D:189 , PHE D:204 , ALA D:205 , LEU D:206 , LYS D:207 , HOH D:435BINDING SITE FOR RESIDUE ARF D 302
47FC2SOFTWARETYR D:148 , GLN D:152BINDING SITE FOR RESIDUE ARF D 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M8L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4M8L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M8L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M8L)

(-) Exons   (0, 0)

(no "Exon" information available for 4M8L)

(-) 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:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh.....hhhhhh.eeeeee...ee.....ee.....hhhhhhhhhhheeeeeeeee.hhh........eeeee...hhhhhhhhhhhh..eeee..........eeeeee.....hhhhhhhhhhh...eeee.ee......eeeee.....eeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m8l A   5 KKNNQDELKKLAATEAAKSITTEITLGVGTGSTVGFLIEELVNYRDKIKTVVSSSEDSTRKLKALGFDVVDLNYAGEIDLYIDGADECNNHKELIKGGGAALTREKICVAAAKKFICIIDESKKVNTLGNFPLPIEVIPMARSYIARQIVKLGGQPVYREQTITDNGNVILDVYNLKIDNPLKLETELNQITGVVTNGIFALKPADTVIMATKDSNIVVL 224
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224


Chain B from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh.....hhhhhh.eeeeee...ee.....ee.....hhhhhhhhhhheeeeeeeee.hhh........eeeee...hhhhhhhhhhhh..eeee..........eeeeee.....hhhhhhhhhhh...eeee.ee......eeeee.....eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m8l B   8 NQDELKKLAATEAAKSITTEITLGVGTGSTVGFLIEELVNYRDKIKTVVSSSEDSTRKLKALGFDVVDLNYAGEIDLYIDGADECNNHKELIKGGGAALTREKICVAAAKKFICIIDESKKVNTLGNFPLPIEVIPMARSYIARQIVKLGGQPVYREQTITDNGNVILDVYNLKIDNPLKLETELNQITGVVTNGIFALKPADTVIMATKDSNIVVL 224
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       


Chain C from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh.....hhhhhh.eeeeee...ee.....ee.....hhhhhhhhhhheeeeeeeee.hhh........eeeee...hhhhhhhhhhhh..eeee..........eeeeee.....hhhhhhhhhhh...eeee.ee......eeeee.....eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m8l C   8 NQDELKKLAATEAAKSITTEITLGVGTGSTVGFLIEELVNYRDKIKTVVSSSEDSTRKLKALGFDVVDLNYAGEIDLYIDGADECNNHKELIKGGGAALTREKICVAAAKKFICIIDESKKVNTLGNFPLPIEVIPMARSYIARQIVKLGGQPVYREQTITDNGNVILDVYNLKIDNPLKLETELNQITGVVTNGIFALKPADTVIMATKDSNIVVL 224
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       


Chain D from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh.....hhhhhh.eeeeee...ee.....ee.....hhhhhhhhhhheeeeeeeee.hhh........eeeee...hhhhhhhhhhhh..eeee..........eeeeee.....hhhhhhhhhhh...eeee.ee......eeeee.....eeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m8l D   7 NNQDELKKLAATEAAKSITTEITLGVGTGSTVGFLIEELVNYRDKIKTVVSSSEDSTRKLKALGFDVVDLNYAGEIDLYIDGADECNNHKELIKGGGAALTREKICVAAAKKFICIIDESKKVNTLGNFPLPIEVIPMARSYIARQIVKLGGQPVYREQTITDNGNVILDVYNLKIDNPLKLETELNQITGVVTNGIFALKPADTVIMATKDSNIVVL 224
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216
   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 4M8L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M8L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M8L)

(-) Gene Ontology  (4, 4)

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3kwm CRYSTAL STRUCTURE OF RIBOSE-5-ISOMERASE A FROM FRANCISELLA TULARENSIS
4io1 CRYSTAL STRUCTURE OF RIBOSE-5-ISOMERASE A FROM FRANCISELLA TULARENSIS RELATED ID: CSGID-IDP02119 RELATED DB: TARGETTRACK