HEADER HYDROLASE INHIBITOR 06-JUN-11 2LE2 TITLE NOVEL DIMERIC STRUCTURE OF PHAGE PHI29-ENCODED PROTEIN P56: INSIGHTS TITLE 2 INTO URACIL-DNA GLYCOSYLASE INHIBITION COMPND MOL_ID: 1; COMPND 2 MOLECULE: P56; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS PHAGE PHI29; SOURCE 3 ORGANISM_TAXID: 10756; SOURCE 4 GENE: 0.8; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PT7-3-P56-PHI29 KEYWDS DNA REPAIR INHIBITION, UDG INHIBITION, DNA MIMICRY, HYDROLASE KEYWDS 2 INHIBITOR EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.ASENSIO,L.PEREZ-LAGO,J.M.LAZARO,C.GONZALEZ,G.SERRANO-HERAS,M.SALAS REVDAT 4 14-JUN-23 2LE2 1 REMARK REVDAT 3 28-DEC-11 2LE2 1 JRNL REVDAT 2 12-OCT-11 2LE2 1 COMPND REVDAT 1 28-SEP-11 2LE2 0 JRNL AUTH J.L.ASENSIO,L.PEREZ-LAGO,J.M.LAZARO,C.GONZALEZ, JRNL AUTH 2 G.SERRANO-HERAS,M.SALAS JRNL TITL NOVEL DIMERIC STRUCTURE OF PHAGE 29-ENCODED PROTEIN P56: JRNL TITL 2 INSIGHTS INTO URACIL-DNA GLYCOSYLASE INHIBITION. JRNL REF NUCLEIC ACIDS RES. V. 39 9779 2011 JRNL REFN ISSN 0305-1048 JRNL PMID 21890898 JRNL DOI 10.1093/NAR/GKR667 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XEASY, AMBER REMARK 3 AUTHORS : BARTELS ET AL. (XEASY), CASE, DARDEN, CHEATHAM, REMARK 3 III, SIMMERLING, WANG, DUKE, LUO, AND KOLLM (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LE2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1000102280. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 5 REMARK 210 IONIC STRENGTH : 0.13 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM P56, 100 MM SODIUM REMARK 210 CHLORIDE, 10 MM SODIUM PHOSPHATE, REMARK 210 90% H2O/10% D2O; 0.5 MM [U-98% REMARK 210 13C; U-98% 15N] P56, 100 MM REMARK 210 SODIUM CHLORIDE, 10 MM SODIUM REMARK 210 PHOSPHATE, 90% H2O/10% D2O; 0.5 REMARK 210 MM P56, 100 MM SODIUM CHLORIDE, REMARK 210 10 MM SODIUM PHOSPHATE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 2D 1H-1H COSY; 2D 1H-15N HSQC; REMARK 210 3D HNCACB; 3D CBCA(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ARG B 51 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 ARG B 51 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 ARG B 51 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 3 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 ARG B 51 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 5 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 6 MET A 1 CG - SD - CE ANGL. DEV. = -11.7 DEGREES REMARK 500 6 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 6 ARG A 51 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 6 ARG B 51 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 8 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 8 ARG B 51 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 ARG B 51 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 10 MET A 14 CG - SD - CE ANGL. DEV. = -10.6 DEGREES REMARK 500 10 ARG B 51 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 11 ARG B 51 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 14 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 14 ARG B 51 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 15 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 15 ARG B 51 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 16 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 17 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 18 ARG B 51 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 19 ARG B 51 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 GLN A 3 96.66 -32.73 REMARK 500 1 ASP A 5 76.87 -151.42 REMARK 500 1 PHE A 6 -32.01 64.63 REMARK 500 1 VAL A 7 87.91 -61.80 REMARK 500 1 ASP A 8 -74.60 -154.52 REMARK 500 1 ALA A 44 -1.78 57.23 REMARK 500 1 GLU A 46 87.51 -64.71 REMARK 500 1 GLN B 3 37.08 -74.35 REMARK 500 1 ASN B 4 10.10 -144.97 REMARK 500 1 ASP B 5 -44.66 -150.83 REMARK 500 1 ASP B 8 -68.30 -141.90 REMARK 500 1 TYR B 10 150.72 -45.84 REMARK 500 1 GLN B 23 157.37 76.76 REMARK 500 1 ALA B 44 29.05 45.09 REMARK 500 1 GLU B 46 93.53 -61.89 REMARK 500 1 ILE B 48 -58.80 -124.89 REMARK 500 2 ASP A 8 178.93 61.91 REMARK 500 2 SER A 9 176.08 65.67 REMARK 500 2 PHE B 6 -28.24 57.87 REMARK 500 2 VAL B 7 158.00 53.53 REMARK 500 2 ASP B 8 -80.38 87.90 REMARK 500 2 ASP B 19 -48.39 67.26 REMARK 500 3 GLN A 3 47.53 -75.88 REMARK 500 3 PHE A 6 40.55 -69.85 REMARK 500 3 SER A 9 175.44 96.54 REMARK 500 3 THR A 43 -74.19 -73.00 REMARK 500 3 ALA A 44 -1.13 52.33 REMARK 500 3 GLU A 46 60.50 61.90 REMARK 500 3 ILE A 48 -69.88 -96.73 REMARK 500 3 ASP B 5 -46.35 -137.05 REMARK 500 3 ASP B 8 -130.63 42.21 REMARK 500 3 SER B 9 -165.24 69.95 REMARK 500 3 ASP B 45 44.06 -76.64 REMARK 500 3 GLU B 46 -126.46 47.98 REMARK 500 3 ILE B 48 -55.68 -123.76 REMARK 500 4 GLN A 3 53.19 -68.07 REMARK 500 4 ASP A 5 -158.34 -129.60 REMARK 500 4 VAL A 7 166.61 54.60 REMARK 500 4 ASP A 8 -79.20 75.21 REMARK 500 4 VAL B 2 -67.00 53.50 REMARK 500 4 ASN B 4 -94.77 49.24 REMARK 500 4 VAL B 7 147.47 -39.65 REMARK 500 4 SER B 9 165.77 76.88 REMARK 500 4 ALA B 44 -9.21 57.81 REMARK 500 5 ASP A 5 33.24 -79.73 REMARK 500 5 VAL A 7 91.68 -66.21 REMARK 500 5 ASP A 8 -80.25 -159.14 REMARK 500 5 ALA A 44 25.48 -65.45 REMARK 500 5 ASP A 45 99.77 -62.96 REMARK 500 5 GLN B 3 28.80 -75.67 REMARK 500 REMARK 500 THIS ENTRY HAS 215 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP A 53 LYS A 54 2 143.75 REMARK 500 ASP B 8 SER B 9 5 -147.43 REMARK 500 LYS A 49 LEU A 50 7 149.72 REMARK 500 LYS A 49 LEU A 50 8 149.71 REMARK 500 ASP B 8 SER B 9 9 -144.52 REMARK 500 SER B 9 TYR B 10 9 149.75 REMARK 500 ASP A 8 SER A 9 13 -143.34 REMARK 500 LEU B 52 ASP B 53 13 149.86 REMARK 500 ASP B 5 PHE B 6 14 137.18 REMARK 500 LYS B 54 VAL B 55 14 149.09 REMARK 500 ASP B 5 PHE B 6 15 -144.63 REMARK 500 ASP A 53 LYS A 54 17 148.22 REMARK 500 ASP B 8 SER B 9 18 -145.00 REMARK 500 ASP B 45 GLU B 46 19 148.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 3 TYR A 25 0.07 SIDE CHAIN REMARK 500 6 ARG A 51 0.08 SIDE CHAIN REMARK 500 7 TYR A 25 0.07 SIDE CHAIN REMARK 500 10 TYR A 25 0.06 SIDE CHAIN REMARK 500 13 TYR B 25 0.08 SIDE CHAIN REMARK 500 17 TYR A 27 0.08 SIDE CHAIN REMARK 500 17 ARG B 51 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17689 RELATED DB: BMRB DBREF 2LE2 A 1 56 UNP Q38503 Q38503_BPPH2 1 56 DBREF 2LE2 B 1 56 UNP Q38503 Q38503_BPPH2 1 56 SEQRES 1 A 56 MET VAL GLN ASN ASP PHE VAL ASP SER TYR ASP VAL THR SEQRES 2 A 56 MET LEU LEU GLN ASP ASP ASP GLY LYS GLN TYR TYR GLU SEQRES 3 A 56 TYR HIS LYS GLY LEU SER LEU SER ASP PHE GLU VAL LEU SEQRES 4 A 56 TYR GLY ASN THR ALA ASP GLU ILE ILE LYS LEU ARG LEU SEQRES 5 A 56 ASP LYS VAL LEU SEQRES 1 B 56 MET VAL GLN ASN ASP PHE VAL ASP SER TYR ASP VAL THR SEQRES 2 B 56 MET LEU LEU GLN ASP ASP ASP GLY LYS GLN TYR TYR GLU SEQRES 3 B 56 TYR HIS LYS GLY LEU SER LEU SER ASP PHE GLU VAL LEU SEQRES 4 B 56 TYR GLY ASN THR ALA ASP GLU ILE ILE LYS LEU ARG LEU SEQRES 5 B 56 ASP LYS VAL LEU HELIX 1 1 SER A 32 THR A 43 1 12 HELIX 2 2 SER B 32 THR B 43 1 12 SHEET 1 A 6 GLN A 23 LEU A 31 0 SHEET 2 A 6 TYR A 10 GLN A 17 -1 N VAL A 12 O HIS A 28 SHEET 3 A 6 ILE A 47 ASP A 53 -1 O ILE A 48 N LEU A 15 SHEET 4 A 6 ILE B 47 ASP B 53 -1 O LEU B 52 N LEU A 50 SHEET 5 A 6 TYR B 10 LEU B 16 -1 N ASP B 11 O ASP B 53 SHEET 6 A 6 TYR B 24 LEU B 31 -1 O GLU B 26 N MET B 14 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1