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(-) Description

Title :  BACILLUS DNA POLYMERASE I LARGE FRAGMENT COMPLEX 1
 
Authors :  W. Wang, L. S. Beese
Date :  02 May 12  (Deposition) - 24 Jul 13  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Dna Polymerase I, Protein-Dna Complex, Closed Form, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Wang, H. W. Hellinga, L. S. Beese
Structures Of A High-Fidelity Dna Polymerase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA POLYMERASE
    Chains: A, D
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: BACILLUS FRAGMENT (ANALOGOUS TO E. COLI KLENOW FRAGMENT, UNP RESIDUES 287-878)
    Gene: POLA, GK2730
    Mutation: YES
    Organism Scientific: GEOBACILLUS KAUSTOPHILUS
    Organism Taxid: 235909
 
Molecule 2 - DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3')
    Chains: B, E
    Engineered: YES
    Other Details: DNA PRIMER STRAND
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*CP*AP*TP*GP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3')
    Chains: C, F
    Engineered: YES
    Other Details: DNA TEMPLATE STRAND
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1DDG2Mod. Nucleotide2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE
2DG32Ligand/Ion2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1DDG1Mod. Nucleotide2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE
2DG31Ligand/Ion2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1DDG1Mod. Nucleotide2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE
2DG31Ligand/Ion2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
3MPD-1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:629 , SER A:655 , GLN A:656 , GLU A:658 , ARG A:702 , LYS A:706 , TYR A:710 , HOH A:1030 , HOH A:1112 , HOH A:1131 , HOH A:1257 , HOH A:1361 , HOH A:1425 , DDG B:29 , DG C:3 , DC C:4BINDING SITE FOR RESIDUE DG3 A 901
2AC2SOFTWAREPRO A:597 , HOH A:1041 , LEU D:352 , LYS D:383 , HOH D:1070BINDING SITE FOR RESIDUE MPD A 902
3AC3SOFTWAREARG D:629 , SER D:655 , GLN D:656 , GLU D:658 , HIS D:682 , ARG D:702 , LYS D:706 , TYR D:710 , HOH D:1001 , HOH D:1038 , HOH D:1096 , HOH D:1199 , HOH D:1218 , HOH D:1243 , HOH D:1483 , HOH D:1676 , DDG E:29 , DG F:3 , DC F:4BINDING SITE FOR RESIDUE DG3 D 901
4AC4SOFTWAREMET D:299 , ALA D:300 , ARG D:343 , ARG D:677BINDING SITE FOR RESIDUE SO4 D 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EZ6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:620 -Pro A:621
2Glu D:620 -Pro D:621

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EZ6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EZ6)

(-) Exons   (0, 0)

(no "Exon" information available for 4EZ6)

(-) 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:549
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4ez6a1 A:297-468 automated matches                                                                                                                                         d4ez6a2 A:469-876 automated matches                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee....hhhhhh.eeeeeee............eeeeee..eeeeehhhhhh.hhhhhhhhh....eeee.hhhhhhhhhhhh......eeeehhhhhhhhhhhhh..hhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh........ee..ee..hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..eee.........eee..........hhhhhhhhh.ee.....eeeeeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...eeeeeee..hhhhhhhhhhhhhhhh........eeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ez6 A 297 AKMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPATKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELRVLAHIAEPNMRRQAKAVNYGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK 876
                                   306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666||     707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867         
                                                                                                                                                                                                                                                                                                                                                                                                            667|                                                                                                                                                                                 
                                                                                                                                                                                                                                                                                                                                                                                                             699                                                                                                                                                                                 


Chain B from PDB  Type:DNA  Length:9
                                         
                 4ez6 B  21 CCTGACTCg  29
                                    |
                                   29-DDG


Chain C from PDB  Type:DNA  Length:11
                                           
                 4ez6 C   2 TGCGAGTCAGG  12
                                    11 


Chain D from PDB  Type:PROTEIN  Length:580
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4ez6d1 D:297-468 automated matches                                                                                                                                         d4ez6d2 D:469-876 automated matches                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...hhhhh..eeeeeee............eeeeee..eeeeehhhhhh.hhhhhhhhhh...eeee.hhhhhhhhhhhh......eeeehhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh........ee..ee..hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.......ee..eee.........eee..........hhhhhhhhh.ee.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...eeeeeee..hhhhhhhhhhhhhhh.........eeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ez6 D 297 AKMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPATKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNYGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK 876
                                   306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876


Chain E from PDB  Type:DNA  Length:9
                                         
                 4ez6 E  21 CCTGACTCg  29
                                    |
                                   29-DDG


Chain F from PDB  Type:DNA  Length:12
                                            
                 4ez6 F   1 ATGCGAGTCAGG  12
                                    10
   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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EZ6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EZ6)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)

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  2.7.7.7
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q5KWC1_GEOKA | Q5KWC1: 2hhq 2hhs 2hht 2hvh 2hw3
UniProtKB/TrEMBL
        Q5KWC1_GEOKA | Q5KWC1: 1njw 1ua0 2hhu 2hhv 2hhw 2hhx 2hvi 3hp6 3pv8 3px0 3px4 3px6 4dqi 4dqp 4dqq 4dqr 4dqs 4ds4 4ds5 4dse 4dsf 4e0d 4ez9 4f2r 4f2s 4f3o 4f4k 4f8r

(-) Related Entries Specified in the PDB File

4ez9 4f2r 4f2s 4f3o 4f4k 4f8r