HEADER DNA BINDING PROTEIN 06-OCT-22 8B9N TITLE CRYSTAL STRUCTURE OF NEI DOMAIN OF MOUSE NEIL3 TRAPPED IN COVALENT TITLE 2 COMPLEX WITH SSDNA WITH ABASIC SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE 8-LIKE 3; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: DNA GLYCOSYLASE FPG2,DNA GLYCOSYLASE/AP LYASE NEIL3, COMPND 5 ENDONUCLEASE VIII-LIKE 3,NEI-LIKE PROTEIN 3; COMPND 6 EC: 3.2.2.-,4.2.99.18; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: SSDNA WITH ABASIC SITE; COMPND 10 CHAIN: B, D; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: NEIL3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 11 ORGANISM_TAXID: 10090 KEYWDS NEIL3, NEI, SSDNA, ABASIC SITE, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.KLIMA,E.BOURA,J.SILHAN REVDAT 1 18-OCT-23 8B9N 0 JRNL AUTH M.KLIMA,E.BOURA,J.SILHAN JRNL TITL CRYSTAL STRUCTURE OF NEI DOMAIN OF MOUSE NEIL3 TRAPPED IN JRNL TITL 2 COVALENT COMPLEX WITH SSDNA WITH ABASIC SITE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20_4459 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 41714 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2082 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 38.2200 - 4.9300 1.00 3032 159 0.2408 0.2828 REMARK 3 2 4.9300 - 3.9100 0.99 2831 149 0.2030 0.2209 REMARK 3 3 3.9100 - 3.4200 0.95 2639 139 0.2418 0.2606 REMARK 3 4 3.4200 - 3.1100 1.00 2780 145 0.2374 0.2919 REMARK 3 5 3.1100 - 2.8800 1.00 2770 146 0.2478 0.2701 REMARK 3 6 2.8800 - 2.7100 1.00 2755 145 0.2366 0.2786 REMARK 3 7 2.7100 - 2.5800 1.00 2732 143 0.2316 0.3089 REMARK 3 8 2.5800 - 2.4700 1.00 2740 144 0.2214 0.2654 REMARK 3 9 2.4700 - 2.3700 1.00 2724 144 0.2360 0.2985 REMARK 3 10 2.3700 - 2.2900 1.00 2714 143 0.2511 0.3361 REMARK 3 11 2.2900 - 2.2200 0.46 1241 63 0.3498 0.4765 REMARK 3 12 2.2200 - 2.1500 1.00 2712 143 0.2652 0.3125 REMARK 3 13 2.1500 - 2.1000 1.00 2699 142 0.2651 0.3188 REMARK 3 14 2.1000 - 2.0500 0.99 2691 142 0.2814 0.3052 REMARK 3 15 2.0500 - 2.0000 0.95 2572 135 0.3302 0.3395 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.275 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.662 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.23 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 : 0.005 3975 REMARK 3 ANGLE : 0.684 5373 REMARK 3 CHIRALITY : 0.048 600 REMARK 3 PLANARITY : 0.006 668 REMARK 3 DIHEDRAL : 13.857 1506 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 8B9N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1292125960. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JAN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43404 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 38.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 23.20 REMARK 200 R MERGE (I) : 0.21920 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 15.00 REMARK 200 R MERGE FOR SHELL (I) : 2.11900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 3W0F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM HEPES.NA PH 7.0, 5 MM MGCL2, 25% REMARK 280 PEG MME 550, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -Y,-X,-Z+1/4 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 110.14600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.07300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 165.21900 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 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 110.14600 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 165.21900 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 55.07300 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 569 LIES ON A SPECIAL POSITION. 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 LEU A 35 REMARK 465 LEU A 36 REMARK 465 GLY A 37 REMARK 465 PRO A 38 REMARK 465 ALA A 39 REMARK 465 MET A 40 REMARK 465 SER A 41 REMARK 465 PRO A 42 REMARK 465 ALA A 43 REMARK 465 ALA A 44 REMARK 465 SER A 45 REMARK 465 PRO A 46 REMARK 465 ALA A 47 REMARK 465 ASP A 48 REMARK 465 VAL A 49 REMARK 465 ALA A 50 REMARK 465 THR A 51 REMARK 465 SER A 52 REMARK 465 ALA A 53 REMARK 465 ALA A 54 REMARK 465 PRO A 55 REMARK 465 MET A 56 REMARK 465 ASN A 57 REMARK 465 ALA A 58 REMARK 465 LYS A 59 REMARK 465 ASP A 60 REMARK 465 SER A 61 REMARK 465 GLY A 62 REMARK 465 TRP A 63 REMARK 465 LYS A 64 REMARK 465 LEU A 65 REMARK 465 LEU A 66 REMARK 465 ARG A 67 REMARK 465 LEU A 68 REMARK 465 PHE A 69 REMARK 465 ASN A 70 REMARK 465 GLY A 71 REMARK 465 TYR A 72 REMARK 465 GLU A 109 REMARK 465 GLY A 110 REMARK 465 GLU A 111 REMARK 465 ASN A 112 REMARK 465 ARG A 113 REMARK 465 GLY A 114 REMARK 465 GLY A 115 REMARK 465 ALA A 116 REMARK 465 GLU A 286 REMARK 465 VAL A 287 REMARK 465 LEU A 288 REMARK 465 PHE A 289 REMARK 465 GLN A 290 REMARK 465 DT B 0 REMARK 465 DT B 16 REMARK 465 DA B 17 REMARK 465 DC B 18 REMARK 465 DG B 19 REMARK 465 GLN C 33 REMARK 465 SER C 34 REMARK 465 LEU C 35 REMARK 465 LEU C 36 REMARK 465 GLY C 37 REMARK 465 PRO C 38 REMARK 465 ALA C 39 REMARK 465 MET C 40 REMARK 465 SER C 41 REMARK 465 PRO C 42 REMARK 465 ALA C 43 REMARK 465 ALA C 44 REMARK 465 SER C 45 REMARK 465 PRO C 46 REMARK 465 ALA C 47 REMARK 465 ASP C 48 REMARK 465 VAL C 49 REMARK 465 ALA C 50 REMARK 465 THR C 51 REMARK 465 SER C 52 REMARK 465 ALA C 53 REMARK 465 ALA C 54 REMARK 465 PRO C 55 REMARK 465 MET C 56 REMARK 465 ASN C 57 REMARK 465 ALA C 58 REMARK 465 LYS C 59 REMARK 465 ASP C 60 REMARK 465 SER C 61 REMARK 465 GLY C 62 REMARK 465 TRP C 63 REMARK 465 LYS C 64 REMARK 465 LEU C 65 REMARK 465 LEU C 66 REMARK 465 ARG C 67 REMARK 465 LEU C 68 REMARK 465 PHE C 69 REMARK 465 ASN C 70 REMARK 465 GLY C 71 REMARK 465 TYR C 72 REMARK 465 ARG C 108 REMARK 465 GLU C 109 REMARK 465 GLY C 110 REMARK 465 GLU C 111 REMARK 465 ASN C 112 REMARK 465 ARG C 113 REMARK 465 GLY C 114 REMARK 465 GLY C 115 REMARK 465 ALA C 116 REMARK 465 GLU C 286 REMARK 465 VAL C 287 REMARK 465 LEU C 288 REMARK 465 PHE C 289 REMARK 465 GLN C 290 REMARK 465 DT D 399 REMARK 465 DC D 400 REMARK 465 DC D 401 REMARK 465 DT D 412 REMARK 465 DA D 413 REMARK 465 DC D 414 REMARK 465 DG D 415 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 GLN A 33 CG CD OE1 NE2 REMARK 470 ARG A 108 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 149 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 220 NE CZ NH1 NH2 REMARK 470 LYS A 245 CD CE NZ REMARK 470 DC B 15 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DC B 15 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC B 15 C6 REMARK 470 LYS C 100 CG CD CE NZ REMARK 470 ARG C 149 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 172 CG CD CE NZ REMARK 470 ARG C 186 NE CZ NH1 NH2 REMARK 470 ARG C 220 NE CZ NH1 NH2 REMARK 470 LYS C 238 CD CE NZ REMARK 470 LYS C 245 CG CD CE NZ REMARK 470 DA D 402 P OP1 OP2 REMARK 470 DC D 411 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DC D 411 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC D 411 C6 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 DA B 3 C3' - O3' - P ANGL. DEV. = -17.6 DEGREES REMARK 500 DRZ B 12 O3' - P - O5' ANGL. DEV. = 11.8 DEGREES REMARK 500 DRZ B 12 O3' - P - OP2 ANGL. DEV. = 13.0 DEGREES REMARK 500 DRZ B 12 C3' - O3' - P ANGL. DEV. = 24.9 DEGREES REMARK 500 DG B 13 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DRZ D 403 O3' - P - OP2 ANGL. DEV. = 18.0 DEGREES REMARK 500 DRZ D 403 C3' - O3' - P ANGL. DEV. = 22.2 DEGREES REMARK 500 DG D 409 O4' - C1' - N9 ANGL. DEV. = 2.5 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 GLU A 3 -169.78 -103.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 629 DISTANCE = 6.00 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 255 SG REMARK 620 2 CYS A 258 SG 108.5 REMARK 620 3 CYS A 277 SG 112.4 96.7 REMARK 620 4 CYS A 280 SG 111.1 111.2 116.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 255 SG REMARK 620 2 CYS C 258 SG 110.4 REMARK 620 3 CYS C 277 SG 109.8 98.0 REMARK 620 4 CYS C 280 SG 110.3 116.0 111.7 REMARK 620 N 1 2 3 DBREF 8B9N A 1 282 UNP Q8K203 NEIL3_MOUSE 1 282 DBREF 8B9N B 0 19 PDB 8B9N 8B9N 0 19 DBREF 8B9N C 1 282 UNP Q8K203 NEIL3_MOUSE 1 282 DBREF 8B9N D 399 415 PDB 8B9N 8B9N 399 415 SEQADV 8B9N PRO A 46 UNP Q8K203 LEU 46 CONFLICT SEQADV 8B9N HIS A 90 UNP Q8K203 PRO 90 CONFLICT SEQADV 8B9N GLY A 114 UNP Q8K203 ALA 114 CONFLICT SEQADV 8B9N GLU A 150 UNP Q8K203 VAL 150 CONFLICT SEQADV 8B9N ARG A 220 UNP Q8K203 CYS 220 CONFLICT SEQADV 8B9N GLY A 256 UNP Q8K203 ASP 256 CONFLICT SEQADV 8B9N ASP A 283 UNP Q8K203 EXPRESSION TAG SEQADV 8B9N GLY A 284 UNP Q8K203 EXPRESSION TAG SEQADV 8B9N LEU A 285 UNP Q8K203 EXPRESSION TAG SEQADV 8B9N GLU A 286 UNP Q8K203 EXPRESSION TAG SEQADV 8B9N VAL A 287 UNP Q8K203 EXPRESSION TAG SEQADV 8B9N LEU A 288 UNP Q8K203 EXPRESSION TAG SEQADV 8B9N PHE A 289 UNP Q8K203 EXPRESSION TAG SEQADV 8B9N GLN A 290 UNP Q8K203 EXPRESSION TAG SEQADV 8B9N PRO C 46 UNP Q8K203 LEU 46 CONFLICT SEQADV 8B9N HIS C 90 UNP Q8K203 PRO 90 CONFLICT SEQADV 8B9N GLY C 114 UNP Q8K203 ALA 114 CONFLICT SEQADV 8B9N GLU C 150 UNP Q8K203 VAL 150 CONFLICT SEQADV 8B9N ARG C 220 UNP Q8K203 CYS 220 CONFLICT SEQADV 8B9N GLY C 256 UNP Q8K203 ASP 256 CONFLICT SEQADV 8B9N ASP C 283 UNP Q8K203 EXPRESSION TAG SEQADV 8B9N GLY C 284 UNP Q8K203 EXPRESSION TAG SEQADV 8B9N LEU C 285 UNP Q8K203 EXPRESSION TAG SEQADV 8B9N GLU C 286 UNP Q8K203 EXPRESSION TAG SEQADV 8B9N VAL C 287 UNP Q8K203 EXPRESSION TAG SEQADV 8B9N LEU C 288 UNP Q8K203 EXPRESSION TAG SEQADV 8B9N PHE C 289 UNP Q8K203 EXPRESSION TAG SEQADV 8B9N GLN C 290 UNP Q8K203 EXPRESSION TAG SEQRES 1 A 290 MET VAL GLU GLY PRO GLY CYS THR LEU ASN GLY GLU LYS SEQRES 2 A 290 ILE ARG ALA ARG VAL LEU PRO GLY GLN ALA VAL THR GLY SEQRES 3 A 290 VAL ARG GLY THR ALA LEU GLN SER LEU LEU GLY PRO ALA SEQRES 4 A 290 MET SER PRO ALA ALA SER PRO ALA ASP VAL ALA THR SER SEQRES 5 A 290 ALA ALA PRO MET ASN ALA LYS ASP SER GLY TRP LYS LEU SEQRES 6 A 290 LEU ARG LEU PHE ASN GLY TYR VAL TYR SER GLY VAL GLU SEQRES 7 A 290 THR LEU GLY LYS GLU LEU PHE MET TYR PHE GLY HIS ARG SEQRES 8 A 290 ALA LEU ARG ILE HIS PHE GLY MET LYS GLY SER ILE LEU SEQRES 9 A 290 ILE ASN PRO ARG GLU GLY GLU ASN ARG GLY GLY ALA SER SEQRES 10 A 290 PRO ALA LEU ALA VAL GLN LEU THR ARG ASP LEU ILE CYS SEQRES 11 A 290 PHE TYR ASP SER SER VAL GLU LEU ARG ASN SER VAL GLU SEQRES 12 A 290 SER GLN GLN ARG VAL ARG GLU MET GLU GLU LEU ASP ILE SEQRES 13 A 290 CYS SER PRO LYS PHE SER PHE SER ARG ALA GLU SER GLU SEQRES 14 A 290 VAL LYS LYS GLN GLY ASP ARG MET LEU CYS ASP VAL LEU SEQRES 15 A 290 LEU ASP GLN ARG VAL LEU PRO GLY VAL GLY ASN ILE ILE SEQRES 16 A 290 LYS ASN GLU ALA LEU PHE ASP SER GLY LEU HIS PRO ALA SEQRES 17 A 290 VAL LYS VAL CYS GLN LEU SER ASP LYS GLN ALA ARG HIS SEQRES 18 A 290 LEU VAL LYS MET THR ARG ASP PHE SER ILE LEU PHE TYR SEQRES 19 A 290 ARG CYS CYS LYS ALA GLY SER ALA ILE SER LYS HIS CYS SEQRES 20 A 290 LYS VAL TYR LYS ARG PRO ASN CYS GLY GLN CYS HIS SER SEQRES 21 A 290 LYS ILE THR VAL CYS ARG PHE GLY GLU ASN SER ARG MET SEQRES 22 A 290 THR TYR PHE CYS PRO HIS CYS GLN LYS ASP GLY LEU GLU SEQRES 23 A 290 VAL LEU PHE GLN SEQRES 1 B 12 DT DC DC DA DRZ DG DT DC DT DA DC DG SEQRES 1 C 290 MET VAL GLU GLY PRO GLY CYS THR LEU ASN GLY GLU LYS SEQRES 2 C 290 ILE ARG ALA ARG VAL LEU PRO GLY GLN ALA VAL THR GLY SEQRES 3 C 290 VAL ARG GLY THR ALA LEU GLN SER LEU LEU GLY PRO ALA SEQRES 4 C 290 MET SER PRO ALA ALA SER PRO ALA ASP VAL ALA THR SER SEQRES 5 C 290 ALA ALA PRO MET ASN ALA LYS ASP SER GLY TRP LYS LEU SEQRES 6 C 290 LEU ARG LEU PHE ASN GLY TYR VAL TYR SER GLY VAL GLU SEQRES 7 C 290 THR LEU GLY LYS GLU LEU PHE MET TYR PHE GLY HIS ARG SEQRES 8 C 290 ALA LEU ARG ILE HIS PHE GLY MET LYS GLY SER ILE LEU SEQRES 9 C 290 ILE ASN PRO ARG GLU GLY GLU ASN ARG GLY GLY ALA SER SEQRES 10 C 290 PRO ALA LEU ALA VAL GLN LEU THR ARG ASP LEU ILE CYS SEQRES 11 C 290 PHE TYR ASP SER SER VAL GLU LEU ARG ASN SER VAL GLU SEQRES 12 C 290 SER GLN GLN ARG VAL ARG GLU MET GLU GLU LEU ASP ILE SEQRES 13 C 290 CYS SER PRO LYS PHE SER PHE SER ARG ALA GLU SER GLU SEQRES 14 C 290 VAL LYS LYS GLN GLY ASP ARG MET LEU CYS ASP VAL LEU SEQRES 15 C 290 LEU ASP GLN ARG VAL LEU PRO GLY VAL GLY ASN ILE ILE SEQRES 16 C 290 LYS ASN GLU ALA LEU PHE ASP SER GLY LEU HIS PRO ALA SEQRES 17 C 290 VAL LYS VAL CYS GLN LEU SER ASP LYS GLN ALA ARG HIS SEQRES 18 C 290 LEU VAL LYS MET THR ARG ASP PHE SER ILE LEU PHE TYR SEQRES 19 C 290 ARG CYS CYS LYS ALA GLY SER ALA ILE SER LYS HIS CYS SEQRES 20 C 290 LYS VAL TYR LYS ARG PRO ASN CYS GLY GLN CYS HIS SER SEQRES 21 C 290 LYS ILE THR VAL CYS ARG PHE GLY GLU ASN SER ARG MET SEQRES 22 C 290 THR TYR PHE CYS PRO HIS CYS GLN LYS ASP GLY LEU GLU SEQRES 23 C 290 VAL LEU PHE GLN SEQRES 1 D 12 DT DC DC DA DRZ DG DT DC DT DA DC DG HET DRZ B 12 11 HET DRZ D 403 11 HET ZN A 401 1 HET ZN C 401 1 HETNAM DRZ 3',4'-DIHYDROXY-PENTANAL-5'-PHOSPHATE HETNAM ZN ZINC ION FORMUL 2 DRZ 2(C5 H11 O7 P) FORMUL 5 ZN 2(ZN 2+) FORMUL 7 HOH *214(H2 O) HELIX 1 AA1 GLU A 3 VAL A 18 1 16 HELIX 2 AA2 SER A 141 GLU A 152 1 12 HELIX 3 AA3 GLU A 153 ASP A 155 5 3 HELIX 4 AA4 SER A 162 LYS A 172 1 11 HELIX 5 AA5 MET A 177 LEU A 183 1 7 HELIX 6 AA6 GLY A 192 SER A 203 1 12 HELIX 7 AA7 LYS A 210 LEU A 214 5 5 HELIX 8 AA8 SER A 215 GLY A 240 1 26 HELIX 9 AA9 ALA A 242 HIS A 246 5 5 HELIX 10 AB1 GLU C 3 VAL C 18 1 16 HELIX 11 AB2 SER C 141 GLU C 152 1 12 HELIX 12 AB3 GLU C 153 ASP C 155 5 3 HELIX 13 AB4 SER C 162 LYS C 172 1 11 HELIX 14 AB5 MET C 177 ASP C 184 1 8 HELIX 15 AB6 GLY C 192 GLY C 204 1 13 HELIX 16 AB7 LYS C 210 LEU C 214 5 5 HELIX 17 AB8 SER C 215 GLY C 240 1 26 HELIX 18 AB9 ALA C 242 CYS C 247 5 6 SHEET 1 AA1 6 VAL A 24 ARG A 28 0 SHEET 2 AA1 6 LEU A 120 LEU A 124 -1 O ALA A 121 N ARG A 28 SHEET 3 AA1 6 LEU A 128 ASN A 140 -1 O ILE A 129 N VAL A 122 SHEET 4 AA1 6 ARG A 91 ILE A 105 -1 N ARG A 94 O GLU A 137 SHEET 5 AA1 6 GLU A 83 PHE A 88 -1 N LEU A 84 O ILE A 95 SHEET 6 AA1 6 GLY A 76 LEU A 80 -1 N GLU A 78 O PHE A 85 SHEET 1 AA2 2 THR A 263 PHE A 267 0 SHEET 2 AA2 2 ARG A 272 PHE A 276 -1 O THR A 274 N CYS A 265 SHEET 1 AA3 6 VAL C 24 ARG C 28 0 SHEET 2 AA3 6 LEU C 120 LEU C 124 -1 O GLN C 123 N GLY C 26 SHEET 3 AA3 6 LEU C 128 ASN C 140 -1 O PHE C 131 N LEU C 120 SHEET 4 AA3 6 ARG C 91 ILE C 105 -1 N ARG C 94 O GLU C 137 SHEET 5 AA3 6 GLU C 83 PHE C 88 -1 N LEU C 84 O ILE C 95 SHEET 6 AA3 6 GLY C 76 LEU C 80 -1 N GLU C 78 O PHE C 85 SHEET 1 AA4 2 THR C 263 PHE C 267 0 SHEET 2 AA4 2 ARG C 272 PHE C 276 -1 O THR C 274 N CYS C 265 LINK N MET A 1 C1' DRZ B 12 1555 1555 1.48 LINK O3' DA B 3 P DRZ B 12 1555 1555 1.56 LINK O3' DRZ B 12 P DG B 13 1555 1555 1.56 LINK N MET C 1 C1' DRZ D 403 1555 1555 1.47 LINK O3' DA D 402 P DRZ D 403 1555 1555 1.56 LINK O3' DRZ D 403 P DG D 409 1555 1555 1.55 LINK SG CYS A 255 ZN ZN A 401 1555 1555 2.34 LINK SG CYS A 258 ZN ZN A 401 1555 1555 2.33 LINK SG CYS A 277 ZN ZN A 401 1555 1555 2.31 LINK SG CYS A 280 ZN ZN A 401 1555 1555 2.31 LINK SG CYS C 255 ZN ZN C 401 1555 1555 2.33 LINK SG CYS C 258 ZN ZN C 401 1555 1555 2.34 LINK SG CYS C 277 ZN ZN C 401 1555 1555 2.31 LINK SG CYS C 280 ZN ZN C 401 1555 1555 2.32 CRYST1 75.056 75.056 220.292 90.00 90.00 90.00 P 41 2 2 16 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 0.013323 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013323 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004539 0.00000