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(-) Description

Title :  CRYSTAL STRUCTURE OF METHYLATED RPA0582 PROTEIN
 
Authors :  P. Sledz, E. Niedzialkowska, M. Chruszcz, P. Porebski, V. Yim, M. Kudri M. D. Zimmerman, E. Evdokimova, A. Savchenko, A. Edwards, A. Joachimi W. Minor, Midwest Center For Structural Genomics (Mcsg)
Date :  15 May 09  (Deposition) - 07 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Alpha-Beta-Barrel, Structural Genomics, Psi-2, Protein Structure Initiative, Reductive Methylation, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Sledz, E. Niedzialkowska, M. Chruszcz, P. Porebski, V. Yim, M. Kudritska, M. D. Zimmerman, E. Evdokimova, A. Savchenko, A. Edwards, A. Joachimiak, W. Minor
Crystal Structure Of Methylated Rpa0582 Protein
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RPA0582
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV LIC
    Expression System Strain: BL21-CODONPLUS(DE3)-RP
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RPA0582
    Mutation: YES
    Organism Scientific: RHODOPSEUDOMONAS PALUSTRIS
    Organism Taxid: 1076
    Strain: CGA009
 
Molecule 2 - RPA0582
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV LIC
    Expression System Strain: BL21-CODONPLUS(DE3)-RP
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RPA0582
    Mutation: YES
    Organism Scientific: RHODOPSEUDOMONAS PALUSTRIS
    Organism Taxid: 1076
    Strain: CGA009
 
Molecule 3 - RPA0582
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV LIC
    Expression System Strain: BL21-CODONPLUS(DE3)-RP
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RPA0582
    Mutation: YES
    Organism Scientific: RHODOPSEUDOMONAS PALUSTRIS
    Organism Taxid: 1076
    Strain: CGA009
 
Molecule 4 - RPA0582
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV LIC
    Expression System Strain: BL21-CODONPLUS(DE3)-RP
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RPA0582
    Mutation: YES
    Organism Scientific: RHODOPSEUDOMONAS PALUSTRIS
    Organism Taxid: 1076
    Strain: CGA009

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (12, 55)

Asymmetric Unit (12, 55)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
22PE2Ligand/IonNONAETHYLENE GLYCOL
3CL4Ligand/IonCHLORIDE ION
4GOL4Ligand/IonGLYCEROL
5MLY7Mod. Amino AcidN-DIMETHYL-LYSINE
6MLZ4Mod. Amino AcidN-METHYL-LYSINE
7MSE16Mod. Amino AcidSELENOMETHIONINE
8PE82Ligand/Ion3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
9PEG7Ligand/IonDI(HYDROXYETHYL)ETHER
10PG42Ligand/IonTETRAETHYLENE GLYCOL
11PGE3Ligand/IonTRIETHYLENE GLYCOL
12SO43Ligand/IonSULFATE ION
Biological Unit 1 (9, 24)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
22PE2Ligand/IonNONAETHYLENE GLYCOL
3CL-1Ligand/IonCHLORIDE ION
4GOL2Ligand/IonGLYCEROL
5MLY4Mod. Amino AcidN-DIMETHYL-LYSINE
6MLZ1Mod. Amino AcidN-METHYL-LYSINE
7MSE8Mod. Amino AcidSELENOMETHIONINE
8PE8-1Ligand/Ion3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
9PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
10PG41Ligand/IonTETRAETHYLENE GLYCOL
11PGE1Ligand/IonTRIETHYLENE GLYCOL
12SO42Ligand/IonSULFATE ION
Biological Unit 2 (10, 27)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
22PE-1Ligand/IonNONAETHYLENE GLYCOL
3CL-1Ligand/IonCHLORIDE ION
4GOL2Ligand/IonGLYCEROL
5MLY3Mod. Amino AcidN-DIMETHYL-LYSINE
6MLZ3Mod. Amino AcidN-METHYL-LYSINE
7MSE8Mod. Amino AcidSELENOMETHIONINE
8PE82Ligand/Ion3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
9PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
10PG41Ligand/IonTETRAETHYLENE GLYCOL
11PGE2Ligand/IonTRIETHYLENE GLYCOL
12SO41Ligand/IonSULFATE ION

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:16 , ARG A:105 , HOH A:164 , ARG B:16 , ARG B:105 , ARG D:16 , ARG D:105BINDING SITE FOR RESIDUE SO4 A 143
02AC2SOFTWAREASP A:19 , ASP B:19 , ASP D:19BINDING SITE FOR RESIDUE SO4 A 144
03AC3SOFTWAREMSE A:26 , ASN A:28 , TYR A:94 , 2PE A:148BINDING SITE FOR RESIDUE CL A 145
04AC4SOFTWAREGLU A:21BINDING SITE FOR RESIDUE PEG A 146
05AC5SOFTWAREGLU A:62 , GLU A:75BINDING SITE FOR RESIDUE PGE A 147
06AC6SOFTWAREASP A:6 , PRO A:7 , ASN A:28 , TYR A:53 , SER A:61 , GLY A:66 , VAL A:68 , TYR A:94 , ILE A:104 , TYR A:109 , ARG A:110 , CL A:145BINDING SITE FOR RESIDUE 2PE A 148
07AC7SOFTWARELEU A:131 , LYS A:132BINDING SITE FOR RESIDUE PEG A 149
08AC8SOFTWARETHR A:2 , GLY A:3 , HIS A:4BINDING SITE FOR RESIDUE GOL A 150
09AC9SOFTWAREMSE B:26 , ASN B:28 , TYR B:94 , PE8 B:148BINDING SITE FOR RESIDUE CL B 143
10BC1SOFTWAREARG B:33BINDING SITE FOR RESIDUE PEG B 144
11BC2SOFTWAREGLU D:21BINDING SITE FOR RESIDUE PEG B 145
12BC3SOFTWAREGLU B:21BINDING SITE FOR RESIDUE PEG B 146
13BC4SOFTWAREGLU B:75 , ARG C:63BINDING SITE FOR RESIDUE PGE B 147
14BC5SOFTWAREASP B:6 , PRO B:7 , ASN B:28 , TYR B:53 , SER B:61 , GLY B:66 , VAL B:68 , TYR B:109 , CL B:143 , HOH B:221 , ILE C:79BINDING SITE FOR RESIDUE PE8 B 148
15BC6SOFTWARETHR B:2 , HIS B:4BINDING SITE FOR RESIDUE GOL B 149
16BC7SOFTWAREARG B:63 , GLU D:75BINDING SITE FOR RESIDUE 1PE B 150
17BC8SOFTWAREARG C:16 , ARG C:105 , HOH C:201BINDING SITE FOR RESIDUE SO4 C 143
18BC9SOFTWAREMSE C:26 , ASN C:28 , TYR C:94 , PE8 C:148BINDING SITE FOR RESIDUE CL C 144
19CC1SOFTWAREVAL B:69 , MLY C:67 , VAL C:69 , GLU C:93 , HOH C:163 , HOH C:227BINDING SITE FOR RESIDUE PG4 C 145
20CC2SOFTWAREGLU C:21BINDING SITE FOR RESIDUE PEG C 146
21CC3SOFTWAREGLU C:75 , GLU D:62 , ARG D:63BINDING SITE FOR RESIDUE PGE C 147
22CC4SOFTWAREASP C:6 , PRO C:7 , ASN C:28 , TYR C:53 , SER C:61 , TYR C:94 , TYR C:109 , ARG C:110 , CL C:144BINDING SITE FOR RESIDUE PE8 C 148
23CC5SOFTWAREGLY C:3 , HIS C:4BINDING SITE FOR RESIDUE GOL C 149
24CC6SOFTWAREMSE D:26 , ASN D:28 , TYR D:94 , 2PE D:146BINDING SITE FOR RESIDUE CL D 143
25CC7SOFTWAREVAL A:69 , VAL D:69 , GLU D:93BINDING SITE FOR RESIDUE PG4 D 144
26CC8SOFTWARELYS D:132 , PRO D:133BINDING SITE FOR RESIDUE PEG D 145
27CC9SOFTWAREASP D:6 , PRO D:7 , ASN D:28 , TYR D:53 , SER D:61 , GLY D:66 , TYR D:109 , CL D:143 , HOH D:222BINDING SITE FOR RESIDUE 2PE D 146
28DC1SOFTWARETHR D:2BINDING SITE FOR RESIDUE GOL D 147

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3HHL)

(-) 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:135
 aligned with Q6NC90_RHOPA | Q6NC90 from UniProtKB/TrEMBL  Length:142

    Alignment length:135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     
         Q6NC90_RHOPA     1 MTGHIDPTKEVFAQFRANDREGPIHMLNLVRLRPRAAYPDGRETTGAEAYAAYGRDSGPVFERLGGKVVWQGQFELMLIGPQDEHWDHVFIAEYPSVAAFVEMIRDPVYREAVKHRQAAVEDSRLIRLKPLKPGK 135
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3hhlA00 A:2-134  [code=3.30.70.900, no name defined]                                                                                 - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh.....eeeeeeeee............hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hhl A   1 mTGHIDPTKEVFAQFRANDREGPIHmLNLVRLRPRAAYPDGRETTGAEAYAAYGRDSGPVSERLGGkVVWQGQFELmLIGPQDEHWDHVFIAEYPSVAAFVEmIRDPVYREAVKHRQAAVEDSRLIRLkPLKPGk 135
                            |       10        20     |  30        40        50        60      | 70      | 80        90       100  |    110       120       130    |
                            |                       26-MSE                                   67-MLY    77-MSE                   103-MSE                   129-MLZ |
                            1-MSE                                                                                                                               135-MLY


Chain B from PDB  Type:PROTEIN  Length:135
 aligned with Q6NC90_RHOPA | Q6NC90 from UniProtKB/TrEMBL  Length:142

    Alignment length:135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     
         Q6NC90_RHOPA     1 MTGHIDPTKEVFAQFRANDREGPIHMLNLVRLRPRAAYPDGRETTGAEAYAAYGRDSGPVFERLGGKVVWQGQFELMLIGPQDEHWDHVFIAEYPSVAAFVEMIRDPVYREAVKHRQAAVEDSRLIRLKPLKPGK 135
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3hhlB00 B:2-134  [code=3.30.70.900, no name defined]                                                                                 - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh.....eeeeeeeee............hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hhl B   1 mTGHIDPTKEVFAQFRANDREGPIHmLNLVRLRPRAAYPDGRETTGAEAYAAYGRDSGPVSERLGGkVVWQGQFELmLIGPQDEHWDHVFIAEYPSVAAFVEmIRDPVYREAVKHRQAAVEDSRLIRLKPLKPGk 135
                            |       10        20     |  30        40        50        60      | 70      | 80        90       100  |    110       120       130    |
                            |                       26-MSE                                   67-MLZ    77-MSE                   103-MSE                         135-MLY
                            1-MSE                                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:135
 aligned with Q6NC90_RHOPA | Q6NC90 from UniProtKB/TrEMBL  Length:142

    Alignment length:135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     
         Q6NC90_RHOPA     1 MTGHIDPTKEVFAQFRANDREGPIHMLNLVRLRPRAAYPDGRETTGAEAYAAYGRDSGPVFERLGGKVVWQGQFELMLIGPQDEHWDHVFIAEYPSVAAFVEMIRDPVYREAVKHRQAAVEDSRLIRLKPLKPGK 135
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3hhlC00 C:2-134  [code=3.30.70.900, no name defined]                                                                                 - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh.....eeeeeeeee............hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hhl C   1 mTGHIDPTKEVFAQFRANDREGPIHmLNLVRLRPRAAYPDGRETTGAEAYAAYGRDSGPVSERLGGkVVWQGQFELmLIGPQDEHWDHVFIAEYPSVAAFVEmIRDPVYREAVkHRQAAVEDSRLIRLkPLKPGk 135
                            |       10        20     |  30        40        50        60      | 70      | 80        90       100  |    110   |   120       130    |
                            |                       26-MSE                                   67-MLY    77-MSE                   103-MSE    114-MLZ        129-MLZ |
                            1-MSE                                                                                                                               135-MLY


Chain D from PDB  Type:PROTEIN  Length:135
 aligned with Q6NC90_RHOPA | Q6NC90 from UniProtKB/TrEMBL  Length:142

    Alignment length:135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     
         Q6NC90_RHOPA     1 MTGHIDPTKEVFAQFRANDREGPIHMLNLVRLRPRAAYPDGRETTGAEAYAAYGRDSGPVFERLGGKVVWQGQFELMLIGPQDEHWDHVFIAEYPSVAAFVEMIRDPVYREAVKHRQAAVEDSRLIRLKPLKPGK 135
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -3hhlD00 D:2-134  [code=3.30.70.900, no name defined]                                                                                 - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh.....eeeeeeeee............hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hhl D   1 mTGHIDPTKEVFAQFRANDREGPIHmLNLVRLRPRAAYPDGRETTGAEAYAAYGRDSGPVSERLGGkVVWQGQFELmLIGPQDEHWDHVFIAEYPSVAAFVEmIRDPVYREAVKHRQAAVEDSRLIRLKPLKPGk 135
                            |       10        20     |  30        40        50        60      | 70      | 80        90       100  |    110       120       130    |
                            |                       26-MSE                                   67-MLY    77-MSE                   103-MSE                         135-MLY
                            1-MSE
   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 3HHL)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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

UniProtKB/TrEMBL
        Q6NC90_RHOPA | Q6NC90: 3dca

(-) Related Entries Specified in the PDB File

3dca NATIVE PROTEIN RELATED ID: APC6229 RELATED DB: TARGETDB