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(-) Description

Title :  THE CRYSTAL STRUCTURE OF YCEI-LIKE FAMILY PROTEIN FROM PSEUDOMONAS SYRINGAE
 
Authors :  Z. Zhang, S. K. Burley, S. Swaminathan, New York Sgx Research Cente Structural Genomics (Nysgxrc)
Date :  21 Dec 10  (Deposition) - 23 Feb 11  (Release) - 23 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, S. K. Burley, S. Swaminathan
The Crystal Structure Of Ycei-Like Family Protein From Pseudomonas Syringae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - YCEI-LIKE FAMILY PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)-CODON+RIL(P)-STRATAGENE
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PSPPH_4050
    Organism Scientific: PSEUDOMONAS SYRINGAE
    Organism Taxid: 264730
    Strain: PV. PHASEOLICOLA

 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, 15)

Asymmetric Unit (3, 15)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MSE8Mod. Amino AcidSELENOMETHIONINE
3UQ84Ligand/IonUBIQUINONE-8
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE4Mod. Amino AcidSELENOMETHIONINE
3UQ82Ligand/IonUBIQUINONE-8
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE4Mod. Amino AcidSELENOMETHIONINE
3UQ82Ligand/IonUBIQUINONE-8

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:32 , PHE A:34 , SER A:36 , LYS A:38 , GLU A:44 , VAL A:55 , ILE A:74 , ARG A:77 , ARG A:80 , ILE A:96 , LEU A:100 , LEU A:120 , LEU A:135 , PHE A:145 , VAL A:147 , LEU A:169 , ALA A:173 , LEU A:175 , VAL A:184 , PHE A:190BINDING SITE FOR RESIDUE UQ8 A 1
2AC2SOFTWAREASN A:27 , GLU A:28 , SER A:30 , HOH A:217 , HOH A:312 , HOH A:497 , LEU B:116 , ARG B:117BINDING SITE FOR RESIDUE GOL A 3
3AC3SOFTWARELEU B:32 , PHE B:34 , LYS B:38 , VAL B:55 , ILE B:74 , ARG B:77 , ARG B:80 , LEU B:81 , ILE B:96 , LEU B:100 , MSE B:102 , PHE B:145 , VAL B:147 , LEU B:153 , LEU B:169 , ALA B:173 , LEU B:175 , VAL B:184 , LYS C:38 , ILE C:42BINDING SITE FOR RESIDUE UQ8 B 2
4AC4SOFTWAREPHE B:91 , VAL B:93 , GLN B:95 , SER B:123 , LEU B:124 , ARG B:125 , GLY B:126 , HOH B:204BINDING SITE FOR RESIDUE GOL B 1
5AC5SOFTWARELYS B:38 , TRP C:23 , LYS C:38 , PHE C:48 , ALA C:61 , ARG C:77 , ARG C:80 , LEU C:100 , LEU C:116 , LEU C:120 , VAL C:147 , MSE C:162 , LEU C:169 , ALA C:173 , LEU C:175 , ALA C:186BINDING SITE FOR RESIDUE UQ8 C 3
6AC6SOFTWAREPHE D:34 , SER D:36 , LYS D:38 , GLU D:44 , PHE D:48 , VAL D:55 , ILE D:74 , ARG D:77 , ARG D:80 , ILE D:96 , LEU D:100 , VAL D:122 , PHE D:145 , VAL D:147 , LEU D:153 , PHE D:166 , LEU D:169 , LEU D:175 , ALA D:186 , PHE D:190BINDING SITE FOR RESIDUE UQ8 D 4
7AC7SOFTWARELEU D:25 , HIS D:52 , GLY D:53 , ARG D:193 , GLY D:195 , HOH D:224 , HOH D:258BINDING SITE FOR RESIDUE GOL D 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q34)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:21 -Asn A:22
2Ala B:21 -Asn B:22

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q34)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q34)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q34)

(-) 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:174
 aligned with Q48EL2_PSE14 | Q48EL2 from UniProtKB/TrEMBL  Length:193

    Alignment length:174
                                                                                                                                                                                                      193 
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  | 
         Q48EL2_PSE14    21 ANWYLDNESSRLSFTSTKNADIAEVHRFLVLHGKVDPKGLAEVEVETESISTGIPLRDERLREQVFQVHKFPVAQINAQLDMRPINNLAPGAQLELRLPLTVSLRGKSHSYNAELLATRLDERRFQVVTLEPLVIHAQDFDMVSDFNALRNAAGLSAVSLSVPVGAVLIFTAR-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee.hhhheeeeeeee...eeeeeee..eeeee....eeeeeee...ee..hhhhhhhhhhhh.......eeeeeee.hhhhhhh.....eeeeeeeeeeee..eeeeeeeeeeeeeee..eeeeee...eeee.hhhhhhhhhhhhhhhh.......eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3q34 A  21 ANWYLDNESSRLSFTSTKNADIAEVHRFLVLHGKVDPKGLAEVEVETESISTGIPLRDERLREQVFQVHKFPVAQINAQLDmRPINNLAPGAQLELRLPLTVSLRGKSHSYNAELLATRLDERRFQVVTLEPLVIHAQDFDmVSDFNALRNAAGLSAVSLSVPVGAVLIFTARE 194
                                    30        40        50        60        70        80        90       100 |     110       120       130       140       150       160 |     170       180       190    
                                                                                                           102-MSE                                                     162-MSE                            


Chain B from PDB  Type:PROTEIN  Length:170
 aligned with Q48EL2_PSE14 | Q48EL2 from UniProtKB/TrEMBL  Length:193

    Alignment length:173
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190   
         Q48EL2_PSE14    21 ANWYLDNESSRLSFTSTKNADIAEVHRFLVLHGKVDPKGLAEVEVETESISTGIPLRDERLREQVFQVHKFPVAQINAQLDMRPINNLAPGAQLELRLPLTVSLRGKSHSYNAELLATRLDERRFQVVTLEPLVIHAQDFDMVSDFNALRNAAGLSAVSLSVPVGAVLIFTAR 193
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhheeeeeeee...eeeeeee..eeeee....eeeeeee...ee..hhhhhhhhhhhh.......eeeeeee.hhhhhhh.....eeeeeeeeeeee..eeeeeeeeeeee..---.eeeeeee.eeee.hhhhhhhhhhhhhhhh.......eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q34 B  21 ANWYLDNESSRLSFTSTKNADIAEVHRFLVLHGKVDPKGLAEVEVETESISTGIPLRDERLREQVFQVHKFPVAQINAQLDmRPINNLAPGAQLELRLPLTVSLRGKSHSYNAELLATRL---RFQVVTLEPLVIHAQDFDmVSDFNALRNAAGLSAVSLSVPVGAVLIFTAR 193
                                    30        40        50        60        70        80        90       100 |     110       120       130       140   |   150       160 |     170       180       190   
                                                                                                           102-MSE                               140 144               162-MSE                           


Chain C from PDB  Type:PROTEIN  Length:171
 aligned with Q48EL2_PSE14 | Q48EL2 from UniProtKB/TrEMBL  Length:193

    Alignment length:171
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191 
         Q48EL2_PSE14    22 NWYLDNESSRLSFTSTKNADIAEVHRFLVLHGKVDPKGLAEVEVETESISTGIPLRDERLREQVFQVHKFPVAQINAQLDMRPINNLAPGAQLELRLPLTVSLRGKSHSYNAELLATRLDERRFQVVTLEPLVIHAQDFDMVSDFNALRNAAGLSAVSLSVPVGAVLIFTA 192
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhheeeeeeee...eeeeeee..eeeee....eeeeeee...ee..hhhhhhhhhhhh.......eeeeeee.hhhhhhh.....eeeeeeeeeeee..eeeeeeeeeeeeeee..eeeeeeee.eeee.hhhhhhhhhhhhhhhh.......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q34 C  22 NWYLDNESSRLSFTSTKNADIAEVHRFLVLHGKVDPKGLAEVEVETESISTGIPLRDERLREQVFQVHKFPVAQINAQLDmRPINNLAPGAQLELRLPLTVSLRGKSHSYNAELLATRLDERRFQVVTLEPLVIHAQDFDmVSDFNALRNAAGLSAVSLSVPVGAVLIFTA 192
                                    31        41        51        61        71        81        91       101|      111       121       131       141       151       161|      171       181       191 
                                                                                                          102-MSE                                                     162-MSE                          


Chain D from PDB  Type:PROTEIN  Length:173
 aligned with Q48EL2_PSE14 | Q48EL2 from UniProtKB/TrEMBL  Length:193

    Alignment length:175
                                                                                                                                                                                                      193  
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  |  
         Q48EL2_PSE14    21 ANWYLDNESSRLSFTSTKNADIAEVHRFLVLHGKVDPKGLAEVEVETESISTGIPLRDERLREQVFQVHKFPVAQINAQLDMRPINNLAPGAQLELRLPLTVSLRGKSHSYNAELLATRLDERRFQVVTLEPLVIHAQDFDMVSDFNALRNAAGLSAVSLSVPVGAVLIFTAR--   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -YceI-3q34D01 D:22-191                                                                                                                                                     ---- Pfam domains (1)
           Pfam domains (2) -YceI-3q34D02 D:22-191                                                                                                                                                     ---- Pfam domains (2)
           Pfam domains (3) -YceI-3q34D03 D:22-191                                                                                                                                                     ---- Pfam domains (3)
           Pfam domains (4) -YceI-3q34D04 D:22-191                                                                                                                                                     ---- Pfam domains (4)
         Sec.struct. author ..eee.hhhheeeeeeee...eeeeeee..eeeee....eeeeeee...ee..hhhhhhhhhhhh.......eeeeeee.hhhhhhh.....eeeeeeeeeeee..eeeeeeeeeeeeeee..eeeeee...eeee.hhhhhhhhhhh..--........eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q34 D  21 ANWYLDNESSRLSFTSTKNADIAEVHRFLVLHGKVDPKGLAEVEVETESISTGIPLRDERLREQVFQVHKFPVAQINAQLDmRPINNLAPGAQLELRLPLTVSLRGKSHSYNAELLATRLDERRFQVVTLEPLVIHAQDFDmVSDFNALR--AGLSAVSLSVPVGAVLIFTAREG 195
                                    30        40        50        60        70        80        90       100 |     110       120       130       140       150       160 |     170  |    180       190     
                                                                                                           102-MSE                                                     162-MSE 170  |                      
                                                                                                                                                                                  173
   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 3Q34)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q34)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: YceI] (5)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3Q34)

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  3q34
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 Related Entries

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