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(-) Description

Title :  CRYSTAL STRUCTURE OF A PERIPLASMIC BINDING PROTEIN (BMA2936) FROM BURKHOLDERIA MALLEI AT 1.80 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  24 Jun 09  (Deposition) - 21 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Type I Periplasmic Binding Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Periplasmic Binding Protein Bma293 (Yp_104442. 1) From Burkholderia Mallei Atcc 23344 At 1. 80 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PERIPLASMIC BRANCHED-CHAIN AMINO ACID-BINDING PROTEIN
    Atcc: 23344
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 25-398
    Gene: BMA2936, YP_104442.1
    Organism Scientific: BURKHOLDERIA MALLEI
    Organism Taxid: 13373
    Synonym: BRANCHED-CHAIN AMINO ACID ABC TRANSPORTER

 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  (4, 50)

Asymmetric Unit (4, 50)
No.NameCountTypeFull Name
1AAE2Ligand/IonACETOACETIC ACID
2CIT6Ligand/IonCITRIC ACID
3EDO14Ligand/Ion1,2-ETHANEDIOL
4MSE28Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (4, 26)
No.NameCountTypeFull Name
1AAE1Ligand/IonACETOACETIC ACID
2CIT3Ligand/IonCITRIC ACID
3EDO8Ligand/Ion1,2-ETHANEDIOL
4MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (4, 24)
No.NameCountTypeFull Name
1AAE1Ligand/IonACETOACETIC ACID
2CIT3Ligand/IonCITRIC ACID
3EDO6Ligand/Ion1,2-ETHANEDIOL
4MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:102 , ASN A:103 , SER A:104 , GLY A:125 , ALA A:126 , GLY A:127 , TYR A:145 , TYR A:173 , PHE A:175BINDING SITE FOR RESIDUE AAE A 501
02AC2SOFTWARETHR B:102 , ASN B:103 , SER B:104 , GLY B:125 , ALA B:126 , GLY B:127 , TYR B:145 , TYR B:173 , PHE B:175BINDING SITE FOR RESIDUE AAE B 501
03AC3SOFTWAREGLY A:0 , CIT A:2 , ALA A:25 , ASP A:26 , SER A:27 , LYS A:29 , GLU A:69 , ARG A:92 , GLY A:93 , GLY A:94 , LYS A:248 , HOH A:471BINDING SITE FOR RESIDUE CIT A 1
04AC4SOFTWARECIT A:1 , CIT A:5 , MSE A:90 , ASP A:91 , ARG A:92 , GLY A:93 , GLY A:94 , GLN A:161 , GLY A:162 , GLY A:163 , GLN A:220 , LYS A:248 , HOH A:570 , HOH A:622 , HOH A:743BINDING SITE FOR RESIDUE CIT A 2
05AC5SOFTWAREGLY B:0 , CIT B:4 , ALA B:25 , LYS B:66 , GLY B:94 , ASP B:96 , GLN B:161 , HOH B:553 , HOH B:641 , HOH B:647 , HOH B:670BINDING SITE FOR RESIDUE CIT B 3
06AC6SOFTWARECIT B:3 , CIT B:6 , MSE B:90 , ASP B:91 , ARG B:92 , GLY B:93 , GLY B:94 , GLN B:161 , GLY B:162 , GLY B:163 , GLN B:220 , LYS B:248 , HOH B:449 , HOH B:674BINDING SITE FOR RESIDUE CIT B 4
07AC7SOFTWAREGLY A:0 , CIT A:2 , LYS A:66 , GLY A:94 , LEU A:95 , ASP A:96 , GLN A:161 , THR A:323 , HOH A:527 , HOH A:547 , HOH A:563 , HOH A:689 , HOH A:743BINDING SITE FOR RESIDUE CIT A 5
08AC8SOFTWAREGLY B:0 , CIT B:4 , ALA B:25 , ASP B:26 , SER B:27 , LYS B:29 , GLU B:69 , ARG B:92 , GLY B:93 , GLY B:94 , LYS B:248 , HOH B:529 , HOH B:572BINDING SITE FOR RESIDUE CIT B 6
09AC9SOFTWAREASP B:42 , ILE B:43 , VAL B:232 , ASN B:257 , ASP B:258 , HOH B:419 , HOH B:614BINDING SITE FOR RESIDUE EDO B 7
10BC1SOFTWAREASP A:42 , ILE A:43 , ASN A:257 , ASP A:258 , HOH A:403 , HOH A:544 , HOH A:717BINDING SITE FOR RESIDUE EDO A 8
11BC2SOFTWARELYS B:248 , GLN B:268 , GLY B:269 , HOH B:513 , HOH B:529BINDING SITE FOR RESIDUE EDO B 9
12BC3SOFTWAREILE A:353 , HIS A:354 , ASP A:355 , GLY A:382BINDING SITE FOR RESIDUE EDO A 10
13BC4SOFTWAREHIS A:260 , TRP A:371 , HOH A:572 , HOH A:649BINDING SITE FOR RESIDUE EDO A 11
14BC5SOFTWARELYS A:53 , ILE A:68 , GLU A:69 , VAL A:70 , HOH A:457BINDING SITE FOR RESIDUE EDO A 12
15BC6SOFTWAREASP A:324 , SER A:325 , ASP A:326 , HOH A:518BINDING SITE FOR RESIDUE EDO A 13
16BC7SOFTWAREGLY B:344 , TYR B:345 , ILE B:353 , HIS B:354 , ASP B:355 , GLY B:382BINDING SITE FOR RESIDUE EDO B 14
17BC8SOFTWARELYS A:78 , ALA A:79 , ASP A:80 , HOH A:542BINDING SITE FOR RESIDUE EDO A 15
18BC9SOFTWAREALA A:283 , ASP A:339 , PHE A:340 , HOH A:710 , HOH A:713 , HOH A:724 , HOH A:765BINDING SITE FOR RESIDUE EDO A 16
19CC1SOFTWAREEDO B:18 , HIS B:260 , GLY B:263 , LEU B:264 , TYR B:373 , HOH B:705BINDING SITE FOR RESIDUE EDO B 17
20CC2SOFTWAREEDO B:17 , TRP B:371 , TYR B:373 , HOH B:524 , HOH B:540BINDING SITE FOR RESIDUE EDO B 18
21CC3SOFTWAREASN B:77 , ASN B:103 , ALA B:105 , TYR B:173 , LEU B:202BINDING SITE FOR RESIDUE EDO B 19
22CC4SOFTWARELEU A:396 , TRP A:397 , LYS A:398 , HOH A:644BINDING SITE FOR RESIDUE EDO A 20

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:136 -A:394
2B:136 -B:394

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3I09)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I09)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3I09)

(-) Exons   (0, 0)

(no "Exon" information available for 3I09)

(-) 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:375
 aligned with A0A0H2WF95_B | A0A0H2WF95 from UniProtKB/TrEMBL  Length:398

    Alignment length:375
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393     
         A0A0H2WF95_B    24 AADSVKIGFITDMSGLYADIDGQGGLEAIKMAVADFGGKVNGKPIEVVYADHQNKADIAASKAREWMDRGGLDLLVGGTNSATALSMNQVAAEKKKVYINIGAGADTLTNEQCTPYTVHYAYDTMALAKGTGSAVVKQGGKTWFFLTADYAFGKALEKNTADVVKANGGKVLGEVRHPLSASDFSSFLLQAQSSKAQILGLANAGGDTVNAIKAAKEFGITKTMKLAALLMFINDVHALGLETTQGLVLTDSWYWNRDQASRQWAQRYFAKMKKMPSSLQAADYSSVTTYLKAVQAAGSTDSDKVMAQLKKMKIDDFYAKGYIRTDGSMIHDMYLMEVKKPSESKEPWDYYKVVATIPGEQAFTTKQETRCALWK 398
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.........hhhhhhhhhhhhhhhhh.ee..eeeeeeeee...hhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhh.eeee....hhhhhh......eee...hhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...ee....eeee.....ee..eeeeee.hhhhh......eeeeeeehhhhhh............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i09 A   0 GADSVKIGFITDmSGLYADIDGQGGLEAIKmAVADFGGKVNGKPIEVVYADHQNKADIAASKAREWmDRGGLDLLVGGTNSATALSmNQVAAEKKKVYINIGAGADTLTNEQCTPYTVHYAYDTmALAKGTGSAVVKQGGKTWFFLTADYAFGKALEKNTADVVKANGGKVLGEVRHPLSASDFSSFLLQAQSSKAQILGLANAGGDTVNAIKAAKEFGITKTmKLAALLmFINDVHALGLETTQGLVLTDSWYWNRDQASRQWAQRYFAKmKKmPSSLQAADYSSVTTYLKAVQAAGSTDSDKVmAQLKKmKIDDFYAKGYIRTDGSmIHDmYLmEVKKPSESKEPWDYYKVVATIPGEQAFTTKQETRCALWK 398
                            ||      33  |     43        53|       63        73        83      | 93       103      |113       123       133       143    |  153       163       173       183       193       203       213       223       233       243   |   253|      263       273       283       293 |  |  303       313       323     | 333 |     343       353  |  | 363       373       383       393     
                            ||         36-MSE            54-MSE                              90-MSE             110-MSE                               148-MSE                                                                                            247-MSE  |                                      295-MSE                           329-MSE |              352-MSE  |                                       
                            0|                                                                                                                                                                                                                                  254-MSE                                     298-MSE                              335-MSE              356-MSE                                      
                            25                                                                                                                                                                                                                                                                                                                                           359-MSE                                   


Chain B from PDB  Type:PROTEIN  Length:375
 aligned with A0A0H2WF95_B | A0A0H2WF95 from UniProtKB/TrEMBL  Length:398

    Alignment length:375
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393     
         A0A0H2WF95_B    24 AADSVKIGFITDMSGLYADIDGQGGLEAIKMAVADFGGKVNGKPIEVVYADHQNKADIAASKAREWMDRGGLDLLVGGTNSATALSMNQVAAEKKKVYINIGAGADTLTNEQCTPYTVHYAYDTMALAKGTGSAVVKQGGKTWFFLTADYAFGKALEKNTADVVKANGGKVLGEVRHPLSASDFSSFLLQAQSSKAQILGLANAGGDTVNAIKAAKEFGITKTMKLAALLMFINDVHALGLETTQGLVLTDSWYWNRDQASRQWAQRYFAKMKKMPSSLQAADYSSVTTYLKAVQAAGSTDSDKVMAQLKKMKIDDFYAKGYIRTDGSMIHDMYLMEVKKPSESKEPWDYYKVVATIPGEQAFTTKQETRCALWK 398
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.........hhhhhhhhhhhhhhhhh.ee..eeeeeeeee...hhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhh.eeee....hhhhhh......eee...hhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...ee....eeee.....ee..eeeeee.hhhhh......eeeeeeehhhhhh.hhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i09 B   0 GADSVKIGFITDmSGLYADIDGQGGLEAIKmAVADFGGKVNGKPIEVVYADHQNKADIAASKAREWmDRGGLDLLVGGTNSATALSmNQVAAEKKKVYINIGAGADTLTNEQCTPYTVHYAYDTmALAKGTGSAVVKQGGKTWFFLTADYAFGKALEKNTADVVKANGGKVLGEVRHPLSASDFSSFLLQAQSSKAQILGLANAGGDTVNAIKAAKEFGITKTmKLAALLmFINDVHALGLETTQGLVLTDSWYWNRDQASRQWAQRYFAKmKKmPSSLQAADYSSVTTYLKAVQAAGSTDSDKVmAQLKKmKIDDFYAKGYIRTDGSmIHDmYLmEVKKPSESKEPWDYYKVVATIPGEQAFTTKQETRCALWK 398
                            ||      33  |     43        53|       63        73        83      | 93       103      |113       123       133       143    |  153       163       173       183       193       203       213       223       233       243   |   253|      263       273       283       293 |  |  303       313       323     | 333 |     343       353  |  | 363       373       383       393     
                            0|         36-MSE            54-MSE                              90-MSE             110-MSE                               148-MSE                                                                                            247-MSE  |                                      295-MSE                           329-MSE |              352-MSE  |                                       
                            25                                                                                                                                                                                                                                  254-MSE                                     298-MSE                              335-MSE              356-MSE                                      
                                                                                                                                                                                                                                                                                                                                                                         359-MSE
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3I09)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3I09)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I09)

(-) Gene Ontology  (0, 0)

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