PDB Short entry for 4HSB HEADER HYDROLASE/DNA 29-OCT-12 4HSB TITLE S. POMBE 3-METHYLADENINE DNA GLYCOSYLASE-LIKE PROTEIN MAG2 BOUND TO TITLE 2 DAMAGED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE DNA-3-METHYLADENINE GLYCOSYLASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 3-METHYLADENINE DNA GLYCOSIDASE 2, 3MEA DNA GLYCOSYLASE 2; COMPND 5 EC: 3.2.2.21; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(P*GP*GP*AP*CP*TP*(3DR)P*AP*CP*GP*GP*G)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(P*CP*CP*CP*GP*TP*TP*AP*GP*TP*CP*C)-3'); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE 972H-; SOURCE 3 ORGANISM_COMMON: FISSION YEAST; SOURCE 4 ORGANISM_TAXID: 284812; SOURCE 5 GENE: SPBC23G7.11; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PBG100; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES KEYWDS HELIX-HAIRPIN-HELIX, NON-SPECIFIC DNA-BINDING MOTIF, HYDROLASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.ADHIKARY,B.F.EICHMAN REVDAT 4 28-FEB-24 4HSB 1 REMARK SEQADV LINK REVDAT 3 01-JAN-14 4HSB 1 REMARK REVDAT 2 10-APR-13 4HSB 1 JRNL REVDAT 1 23-JAN-13 4HSB 0 JRNL AUTH S.ADHIKARY,M.C.CATO,K.L.MCGARY,A.ROKAS,B.F.EICHMAN JRNL TITL NON-PRODUCTIVE DNA DAMAGE BINDING BY DNA GLYCOSYLASE-LIKE JRNL TITL 2 PROTEIN MAG2 FROM SCHIZOSACCHAROMYCES POMBE. JRNL REF DNA REPAIR V. 12 196 2013 JRNL REFN ISSN 1568-7864 JRNL PMID 23273506 JRNL DOI 10.1016/J.DNAREP.2012.12.001 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 22187 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1121 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.8584 - 3.7800 0.99 2824 132 0.2079 0.2284 REMARK 3 2 3.7800 - 3.0012 1.00 2683 133 0.1954 0.2491 REMARK 3 3 3.0012 - 2.6221 1.00 2610 159 0.1897 0.2488 REMARK 3 4 2.6221 - 2.3825 1.00 2614 132 0.1760 0.2200 REMARK 3 5 2.3825 - 2.2117 1.00 2618 138 0.1714 0.2288 REMARK 3 6 2.2117 - 2.0814 1.00 2606 131 0.1679 0.2223 REMARK 3 7 2.0814 - 1.9772 1.00 2569 156 0.1795 0.2340 REMARK 3 8 1.9772 - 1.8911 0.99 2542 140 0.1960 0.2318 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.750 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 2157 REMARK 3 ANGLE : 1.117 3000 REMARK 3 CHIRALITY : 0.070 338 REMARK 3 PLANARITY : 0.005 303 REMARK 3 DIHEDRAL : 21.017 848 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 5 THROUGH 40 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.0583 -2.1590 2.5761 REMARK 3 T TENSOR REMARK 3 T11: 0.2258 T22: 0.1609 REMARK 3 T33: 0.2055 T12: 0.0041 REMARK 3 T13: 0.0447 T23: -0.0642 REMARK 3 L TENSOR REMARK 3 L11: 1.6330 L22: 2.1868 REMARK 3 L33: 4.4852 L12: -0.2170 REMARK 3 L13: -0.3909 L23: -0.6426 REMARK 3 S TENSOR REMARK 3 S11: -0.0300 S12: -0.2861 S13: 0.1622 REMARK 3 S21: 0.5433 S22: -0.0014 S23: 0.2906 REMARK 3 S31: -0.3427 S32: -0.1386 S33: 0.0230 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 41 THROUGH 162 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.4815 -6.3800 -20.8299 REMARK 3 T TENSOR REMARK 3 T11: 0.1514 T22: 0.1729 REMARK 3 T33: 0.1336 T12: 0.0001 REMARK 3 T13: 0.0085 T23: 0.0300 REMARK 3 L TENSOR REMARK 3 L11: 2.7783 L22: 2.4775 REMARK 3 L33: 2.7235 L12: 0.0839 REMARK 3 L13: -1.6629 L23: -0.0136 REMARK 3 S TENSOR REMARK 3 S11: -0.0416 S12: 0.1277 S13: 0.0451 REMARK 3 S21: -0.2890 S22: -0.0601 S23: -0.1812 REMARK 3 S31: 0.0111 S32: 0.2366 S33: 0.0836 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 163 THROUGH 209 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.5378 -14.7451 0.0779 REMARK 3 T TENSOR REMARK 3 T11: 0.1701 T22: 0.1482 REMARK 3 T33: 0.1450 T12: 0.0058 REMARK 3 T13: 0.0578 T23: 0.0215 REMARK 3 L TENSOR REMARK 3 L11: 2.3008 L22: 6.2949 REMARK 3 L33: 2.2138 L12: 0.6041 REMARK 3 L13: -0.6487 L23: -0.0533 REMARK 3 S TENSOR REMARK 3 S11: -0.0516 S12: -0.1767 S13: -0.2189 REMARK 3 S21: 0.2474 S22: 0.0358 S23: 0.2155 REMARK 3 S31: 0.2333 S32: -0.1638 S33: 0.0105 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 2 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.6180 -26.3944 -6.7014 REMARK 3 T TENSOR REMARK 3 T11: 1.8357 T22: 2.3432 REMARK 3 T33: 1.0913 T12: 0.2620 REMARK 3 T13: -0.3378 T23: 0.5731 REMARK 3 L TENSOR REMARK 3 L11: 6.5067 L22: 1.5273 REMARK 3 L33: 2.2381 L12: -1.5440 REMARK 3 L13: 3.5618 L23: -0.2601 REMARK 3 S TENSOR REMARK 3 S11: 0.8764 S12: 0.4305 S13: -1.3741 REMARK 3 S21: 0.8626 S22: -0.3237 S23: -0.4218 REMARK 3 S31: 1.2869 S32: 1.1163 S33: -0.5264 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 7 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.9359 -22.8054 -21.4294 REMARK 3 T TENSOR REMARK 3 T11: 0.6562 T22: 0.3112 REMARK 3 T33: 0.4223 T12: 0.1773 REMARK 3 T13: 0.1453 T23: 0.0613 REMARK 3 L TENSOR REMARK 3 L11: 8.5443 L22: 3.2842 REMARK 3 L33: 2.6541 L12: 0.1119 REMARK 3 L13: 0.2163 L23: 1.8919 REMARK 3 S TENSOR REMARK 3 S11: -0.0568 S12: 0.0440 S13: -1.4563 REMARK 3 S21: 0.2553 S22: 0.0298 S23: -0.4110 REMARK 3 S31: 1.5532 S32: 0.6341 S33: -0.1509 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 2 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.7932 -29.2648 -18.5910 REMARK 3 T TENSOR REMARK 3 T11: 0.8210 T22: 0.6904 REMARK 3 T33: 0.8234 T12: 0.2136 REMARK 3 T13: 0.3136 T23: 0.2176 REMARK 3 L TENSOR REMARK 3 L11: 2.8613 L22: 2.0242 REMARK 3 L33: 8.6718 L12: 1.4545 REMARK 3 L13: 4.6043 L23: 2.4982 REMARK 3 S TENSOR REMARK 3 S11: 0.3755 S12: -0.5875 S13: -1.1903 REMARK 3 S21: 0.7383 S22: -0.4069 S23: 0.6563 REMARK 3 S31: 1.4350 S32: -0.6623 S33: 0.0888 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 7 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.8507 -17.5864 -7.3516 REMARK 3 T TENSOR REMARK 3 T11: 1.0436 T22: 1.4312 REMARK 3 T33: 0.6806 T12: 0.5071 REMARK 3 T13: -0.1862 T23: 0.3624 REMARK 3 L TENSOR REMARK 3 L11: 2.6120 L22: 4.7810 REMARK 3 L33: 7.2248 L12: 2.0409 REMARK 3 L13: 3.0183 L23: -1.0795 REMARK 3 S TENSOR REMARK 3 S11: -0.5223 S12: -1.8049 S13: -0.2799 REMARK 3 S21: 2.0264 S22: -0.0772 S23: -0.8892 REMARK 3 S31: -0.5679 S32: 0.0859 S33: 0.4717 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4HSB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000075858. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 REMARK 200 MONOCHROMATOR : C(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22239 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 51.152 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 30.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM HEPES, 200 MM KCL, 25 MM MGSO4 , REMARK 280 PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 102.30467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 51.15233 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 51.15233 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 102.30467 REMARK 290 REMARK 290 REMARK: NULL 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -3 REMARK 465 PRO A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 LYS A 3 REMARK 465 ASP A 4 REMARK 465 ARG A 210 REMARK 465 LYS A 211 REMARK 465 GLY A 212 REMARK 465 GLN A 213 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 8 CG CD CE NZ REMARK 470 ASN A 19 CG OD1 ND2 REMARK 470 LYS A 53 CG CD CE NZ REMARK 470 ASP A 56 CG OD1 OD2 REMARK 470 GLU A 75 CD OE1 OE2 REMARK 470 LYS A 80 CG CD CE NZ 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 DG B 2 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG B 3 O4' - C4' - C3' ANGL. DEV. = -2.9 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 LYS A 140 -158.58 -127.43 REMARK 500 THR A 151 -64.10 -101.25 REMARK 500 PRO A 193 30.31 -99.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3S6I RELATED DB: PDB REMARK 900 RELATED DNA GLYCOSYLASE FROM S. POMBE (MAG1) DBREF 4HSB A 1 213 UNP O94468 MAG2_SCHPO 1 213 DBREF 4HSB B 2 12 PDB 4HSB 4HSB 2 12 DBREF 4HSB C 2 12 PDB 4HSB 4HSB 2 12 SEQADV 4HSB GLY A -3 UNP O94468 EXPRESSION TAG SEQADV 4HSB PRO A -2 UNP O94468 EXPRESSION TAG SEQADV 4HSB GLY A -1 UNP O94468 EXPRESSION TAG SEQADV 4HSB SER A 0 UNP O94468 EXPRESSION TAG SEQRES 1 A 217 GLY PRO GLY SER MET SER LYS ASP SER ASP TYR LYS ARG SEQRES 2 A 217 ALA GLU LYS HIS LEU SER SER ILE ASP ASN LYS TRP SER SEQRES 3 A 217 SER LEU VAL LYS LYS VAL GLY PRO CYS THR LEU THR PRO SEQRES 4 A 217 HIS PRO GLU HIS ALA PRO TYR GLU GLY ILE ILE ARG ALA SEQRES 5 A 217 ILE THR SER GLN LYS LEU SER ASP ALA ALA THR ASN SER SEQRES 6 A 217 ILE ILE ASN LYS PHE CYS THR GLN CYS SER ASP ASN ASP SEQRES 7 A 217 GLU PHE PRO THR PRO LYS GLN ILE MET GLU THR ASP VAL SEQRES 8 A 217 GLU THR LEU HIS GLU CYS GLY PHE SER LYS LEU LYS SER SEQRES 9 A 217 GLN GLU ILE HIS ILE VAL ALA GLU ALA ALA LEU ASN LYS SEQRES 10 A 217 GLN ILE PRO SER LYS SER GLU ILE GLU LYS MET SER GLU SEQRES 11 A 217 GLU GLU LEU MET GLU SER LEU SER LYS ILE LYS GLY VAL SEQRES 12 A 217 LYS ARG TRP THR ILE GLU MET TYR SER ILE PHE THR LEU SEQRES 13 A 217 GLY ARG LEU ASP ILE MET PRO ALA ASP ASP SER THR LEU SEQRES 14 A 217 LYS ASN GLU ALA LYS GLU PHE PHE GLY LEU SER SER LYS SEQRES 15 A 217 PRO GLN THR GLU GLU VAL GLU LYS LEU THR LYS PRO CYS SEQRES 16 A 217 LYS PRO TYR ARG THR ILE ALA ALA TRP TYR LEU TRP GLN SEQRES 17 A 217 ILE PRO LYS LEU HIS ARG LYS GLY GLN SEQRES 1 B 11 DG DG DA DC DT 3DR DA DC DG DG DG SEQRES 1 C 11 DC DC DC DG DT DT DA DG DT DC DC HET 3DR B 7 11 HET PEG A 301 7 HET PEG A 302 7 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 2 3DR C5 H11 O6 P FORMUL 4 PEG 2(C4 H10 O3) FORMUL 6 HOH *114(H2 O) HELIX 1 1 SER A 5 SER A 16 1 12 HELIX 2 2 ASP A 18 GLY A 29 1 12 HELIX 3 3 ALA A 40 GLN A 52 1 13 HELIX 4 4 SER A 55 SER A 71 1 17 HELIX 5 5 THR A 78 GLU A 84 1 7 HELIX 6 6 ASP A 86 GLU A 92 1 7 HELIX 7 7 SER A 96 ASN A 112 1 17 HELIX 8 8 SER A 117 GLU A 122 1 6 HELIX 9 9 SER A 125 SER A 134 1 10 HELIX 10 10 LYS A 140 THR A 151 1 12 HELIX 11 11 ASP A 162 PHE A 173 1 12 HELIX 12 12 GLN A 180 THR A 188 1 9 HELIX 13 13 LYS A 189 LYS A 192 5 4 HELIX 14 14 TYR A 194 GLN A 204 1 11 HELIX 15 15 ILE A 205 HIS A 209 5 5 LINK O3' DT B 6 P 3DR B 7 1555 1555 1.61 LINK O3' 3DR B 7 P DA B 8 1555 1555 1.60 CISPEP 1 LYS A 192 PRO A 193 0 7.77 SITE 1 AC1 1 PRO A 193 SITE 1 AC2 3 LYS A 20 LYS A 27 LEU A 208 CRYST1 54.891 54.891 153.457 90.00 90.00 120.00 P 32 2 1 6 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 0.018218 0.010518 0.000000 0.00000 SCALE2 0.000000 0.021036 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006516 0.00000