HEADER DNA BINDING PROTEIN/DNA 07-FEB-20 6LWF TITLE CRYSTAL STRUCTURE OF HUMAN NEIL1(P2G, E3Q, K242) BOUND TO DUPLEX DNA TITLE 2 CONTAINING GUANIDINOHYDANTOIN (GH) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE 8-LIKE 1; COMPND 3 CHAIN: A, D; COMPND 4 SYNONYM: DNA GLYCOSYLASE/AP LYASE NEIL1,DNA-(APURINIC OR APYRIMIDINIC COMPND 5 SITE) LYASE NEIL1,ENDONUCLEASE VIII-LIKE 1,FPG1,NEI HOMOLOG 1,NEH1, COMPND 6 NEI-LIKE PROTEIN 1; COMPND 7 EC: 3.2.2.-,4.2.99.18; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: DNA (5'-D(*CP*GP*TP*CP*CP*AP*(DGH)P*GP*TP*CP*TP*AP*C)-3'); COMPND 12 CHAIN: B, E; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: OLIGO DNA CONTAINING GH; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3'); COMPND 17 CHAIN: C, F; COMPND 18 ENGINEERED: YES; COMPND 19 OTHER_DETAILS: COMPLEMENTARY STRAND SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NEIL1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 11 ORGANISM_TAXID: 562; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 15 ORGANISM_TAXID: 562 KEYWDS COMPLEX, BASE LESION, OXIDATIVE DNA DAMAGE, DNA REPAIR, DNA BINDING KEYWDS 2 PROTEIN, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.H.LIU,J.ZHANG,C.X.ZHU,X.X.ZHANG,Y.Q.GAO,C.Q.YI REVDAT 3 29-NOV-23 6LWF 1 REMARK REVDAT 2 14-JUL-21 6LWF 1 JRNL REVDAT 1 09-JUN-21 6LWF 0 JRNL AUTH M.LIU,J.ZHANG,C.ZHU,X.ZHANG,W.XIAO,Y.YAN,L.LIU,H.ZENG, JRNL AUTH 2 Y.Q.GAO,C.YI JRNL TITL DNA REPAIR GLYCOSYLASE HNEIL1 TRIAGES DAMAGED BASES VIA JRNL TITL 2 COMPETING INTERACTION MODES. JRNL REF NAT COMMUN V. 12 4108 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34226550 JRNL DOI 10.1038/S41467-021-24431-Y REMARK 2 REMARK 2 RESOLUTION. 2.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 21772 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1106 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.79 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1568 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.3060 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4152 REMARK 3 NUCLEIC ACID ATOMS : 1054 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 65 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 106.9 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.07000 REMARK 3 B22 (A**2) : 2.67000 REMARK 3 B33 (A**2) : 3.40000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 1.563 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.341 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.286 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 31.404 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5463 ; 0.008 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 4625 ; 0.002 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7595 ; 1.701 ; 1.550 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10649 ; 1.319 ; 1.763 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 526 ;13.700 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 260 ;30.873 ;19.769 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 682 ;17.920 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 50 ;19.784 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 648 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5553 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1383 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 289 REMARK 3 ORIGIN FOR THE GROUP (A): -67.952 308.899 100.652 REMARK 3 T TENSOR REMARK 3 T11: 0.0606 T22: 0.0837 REMARK 3 T33: 0.0942 T12: -0.0267 REMARK 3 T13: 0.0253 T23: 0.0098 REMARK 3 L TENSOR REMARK 3 L11: 6.8981 L22: 2.1077 REMARK 3 L33: 3.6936 L12: 0.2439 REMARK 3 L13: 1.5491 L23: 0.1018 REMARK 3 S TENSOR REMARK 3 S11: 0.0894 S12: -0.5071 S13: -0.4445 REMARK 3 S21: 0.1221 S22: -0.0242 S23: 0.3244 REMARK 3 S31: 0.4124 S32: -0.1255 S33: -0.0652 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 13 REMARK 3 ORIGIN FOR THE GROUP (A): -75.204 293.049 106.138 REMARK 3 T TENSOR REMARK 3 T11: 0.5753 T22: 0.4409 REMARK 3 T33: 0.6428 T12: -0.1770 REMARK 3 T13: 0.0825 T23: 0.1152 REMARK 3 L TENSOR REMARK 3 L11: 2.7930 L22: 3.4685 REMARK 3 L33: 10.7474 L12: -0.1029 REMARK 3 L13: -1.2898 L23: -2.9093 REMARK 3 S TENSOR REMARK 3 S11: -0.2669 S12: -0.3025 S13: -0.9783 REMARK 3 S21: 0.3032 S22: 0.1701 S23: 0.3061 REMARK 3 S31: 1.7544 S32: -0.2598 S33: 0.0968 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 13 REMARK 3 ORIGIN FOR THE GROUP (A): -77.777 293.197 110.626 REMARK 3 T TENSOR REMARK 3 T11: 0.5811 T22: 0.4962 REMARK 3 T33: 0.7157 T12: -0.0368 REMARK 3 T13: 0.1390 T23: 0.2921 REMARK 3 L TENSOR REMARK 3 L11: 12.1564 L22: 3.8060 REMARK 3 L33: 7.3164 L12: 2.8546 REMARK 3 L13: 2.4098 L23: -0.5846 REMARK 3 S TENSOR REMARK 3 S11: 0.2066 S12: -0.5215 S13: -1.0964 REMARK 3 S21: -0.3735 S22: 0.0219 S23: 0.7258 REMARK 3 S31: 0.1689 S32: -0.6513 S33: -0.2285 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 2 D 289 REMARK 3 ORIGIN FOR THE GROUP (A): -64.228 332.292 79.571 REMARK 3 T TENSOR REMARK 3 T11: 0.3328 T22: 0.3301 REMARK 3 T33: 0.2283 T12: -0.0965 REMARK 3 T13: 0.1379 T23: 0.0034 REMARK 3 L TENSOR REMARK 3 L11: 3.9780 L22: 6.9573 REMARK 3 L33: 4.7795 L12: 0.2086 REMARK 3 L13: -0.9472 L23: 1.5837 REMARK 3 S TENSOR REMARK 3 S11: 0.3103 S12: 0.1361 S13: 0.7061 REMARK 3 S21: -0.2192 S22: -0.2293 S23: -0.2118 REMARK 3 S31: -0.7194 S32: 0.1517 S33: -0.0811 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 1 E 13 REMARK 3 ORIGIN FOR THE GROUP (A): -53.965 346.196 71.919 REMARK 3 T TENSOR REMARK 3 T11: 1.2162 T22: 0.8946 REMARK 3 T33: 1.0016 T12: -0.0832 REMARK 3 T13: 0.0834 T23: 0.1851 REMARK 3 L TENSOR REMARK 3 L11: 0.3355 L22: 0.8997 REMARK 3 L33: 10.4324 L12: -0.4497 REMARK 3 L13: 1.4607 L23: -1.4411 REMARK 3 S TENSOR REMARK 3 S11: 0.0036 S12: 0.3151 S13: 0.3144 REMARK 3 S21: -0.0245 S22: -0.3271 S23: -0.3621 REMARK 3 S31: -0.7065 S32: 1.0103 S33: 0.3234 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 1 F 13 REMARK 3 ORIGIN FOR THE GROUP (A): -55.757 348.262 67.124 REMARK 3 T TENSOR REMARK 3 T11: 1.1198 T22: 1.0510 REMARK 3 T33: 0.8475 T12: 0.0007 REMARK 3 T13: 0.0435 T23: 0.1574 REMARK 3 L TENSOR REMARK 3 L11: 2.7734 L22: 12.7728 REMARK 3 L33: 3.9517 L12: 1.3568 REMARK 3 L13: -2.5906 L23: 2.6402 REMARK 3 S TENSOR REMARK 3 S11: 0.6017 S12: -0.2515 S13: 0.6940 REMARK 3 S21: -0.4753 S22: 0.1259 S23: -0.4724 REMARK 3 S31: -0.9865 S32: -0.0756 S33: -0.7276 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6LWF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1300015554. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 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 : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22914 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.790 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.99900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: 5ITY REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS REMARK 200 COLUMNS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CACODYLIC ACID (PH 6.5), 0.1 M REMARK 280 NACL, 0.05 M MGCL2 AND 18% (W/V) PEG 8000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 44.30200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 71.28200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.30200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 71.28200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 3190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F 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 MET A 1 REMARK 465 GLN A 203 REMARK 465 HIS A 204 REMARK 465 ARG A 205 REMARK 465 PRO A 206 REMARK 465 SER A 207 REMARK 465 PRO A 208 REMARK 465 GLU A 209 REMARK 465 LEU A 210 REMARK 465 THR A 211 REMARK 465 LEU A 212 REMARK 465 SER A 213 REMARK 465 GLN A 214 REMARK 465 LYS A 215 REMARK 465 ILE A 216 REMARK 465 ARG A 217 REMARK 465 THR A 218 REMARK 465 LYS A 219 REMARK 465 LEU A 220 REMARK 465 GLN A 221 REMARK 465 GLU A 247 REMARK 465 SER A 248 REMARK 465 GLY A 249 REMARK 465 PRO A 290 REMARK 465 LYS A 291 REMARK 465 GLY A 292 REMARK 465 ARG A 293 REMARK 465 LYS A 294 REMARK 465 SER A 295 REMARK 465 MET D 1 REMARK 465 LEU D 201 REMARK 465 GLN D 202 REMARK 465 GLN D 203 REMARK 465 HIS D 204 REMARK 465 ARG D 205 REMARK 465 PRO D 206 REMARK 465 SER D 207 REMARK 465 PRO D 208 REMARK 465 GLU D 209 REMARK 465 LEU D 210 REMARK 465 THR D 211 REMARK 465 LEU D 212 REMARK 465 SER D 213 REMARK 465 GLN D 214 REMARK 465 LYS D 215 REMARK 465 ILE D 216 REMARK 465 ARG D 217 REMARK 465 THR D 218 REMARK 465 LYS D 219 REMARK 465 LEU D 220 REMARK 465 GLN D 221 REMARK 465 ASN D 222 REMARK 465 SER D 246 REMARK 465 GLU D 247 REMARK 465 SER D 248 REMARK 465 PRO D 290 REMARK 465 LYS D 291 REMARK 465 GLY D 292 REMARK 465 ARG D 293 REMARK 465 LYS D 294 REMARK 465 SER D 295 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 ALA A 289 CB REMARK 470 ALA D 44 CB REMARK 470 ALA D 66 CB REMARK 470 GLN D 69 CB CG CD OE1 NE2 REMARK 470 ALA D 104 CB REMARK 470 LYS D 155 CB CG CD CE NZ REMARK 470 GLU D 163 CB CG CD OE1 OE2 REMARK 470 ALA D 164 CB REMARK 470 SER D 196 CB OG REMARK 470 LEU D 198 CG CD1 CD2 REMARK 470 GLU D 199 CB CG CD OE1 OE2 REMARK 470 GLU D 251 CB CG CD OE1 OE2 REMARK 470 ALA D 258 CB REMARK 470 LEU D 271 CG CD1 CD2 REMARK 470 PRO D 287 CB CG CD REMARK 470 ALA D 289 CB REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OH TYR D 263 OP1 8Y9 E 7 2.11 REMARK 500 OE1 GLU A 28 OH TYR A 102 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 227 CD GLU A 227 OE2 0.073 REMARK 500 GLY D 283 C GLY D 283 O 0.101 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 GLN A 3 -163.67 -110.63 REMARK 500 ALA A 44 119.55 -167.25 REMARK 500 HIS A 96 17.48 80.70 REMARK 500 ALA A 97 99.89 -69.76 REMARK 500 ASP A 116 87.40 -154.32 REMARK 500 ASN A 172 109.97 -55.39 REMARK 500 ASP A 252 -16.78 -48.36 REMARK 500 CYS A 262 -67.60 -135.16 REMARK 500 SER A 270 117.16 -161.59 REMARK 500 LEU A 271 -155.66 -108.62 REMARK 500 ALA D 44 115.34 -166.41 REMARK 500 GLU D 92 55.19 -118.94 REMARK 500 HIS D 96 20.30 80.84 REMARK 500 ASP D 116 86.72 -153.28 REMARK 500 ASN D 172 109.36 -56.74 REMARK 500 CYS D 262 -70.42 -134.60 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 PRO A 105 PRO A 106 30.98 REMARK 500 PRO D 105 PRO D 106 57.55 REMARK 500 REMARK 500 REMARK: NULL DBREF 6LWF A 1 295 UNP Q96FI4 NEIL1_HUMAN 1 295 DBREF 6LWF B 1 13 PDB 6LWF 6LWF 1 13 DBREF 6LWF C 1 13 PDB 6LWF 6LWF 1 13 DBREF 6LWF D 1 295 UNP Q96FI4 NEIL1_HUMAN 1 295 DBREF 6LWF E 1 13 PDB 6LWF 6LWF 1 13 DBREF 6LWF F 1 13 PDB 6LWF 6LWF 1 13 SEQADV 6LWF GLY A 2 UNP Q96FI4 PRO 2 ENGINEERED MUTATION SEQADV 6LWF GLN A 3 UNP Q96FI4 GLU 3 ENGINEERED MUTATION SEQADV 6LWF GLY D 2 UNP Q96FI4 PRO 2 ENGINEERED MUTATION SEQADV 6LWF GLN D 3 UNP Q96FI4 GLU 3 ENGINEERED MUTATION SEQRES 1 A 295 MET GLY GLN GLY PRO GLU LEU HIS LEU ALA SER GLN PHE SEQRES 2 A 295 VAL ASN GLU ALA CYS ARG ALA LEU VAL PHE GLY GLY CYS SEQRES 3 A 295 VAL GLU LYS SER SER VAL SER ARG ASN PRO GLU VAL PRO SEQRES 4 A 295 PHE GLU SER SER ALA TYR ARG ILE SER ALA SER ALA ARG SEQRES 5 A 295 GLY LYS GLU LEU ARG LEU ILE LEU SER PRO LEU PRO GLY SEQRES 6 A 295 ALA GLN PRO GLN GLN GLU PRO LEU ALA LEU VAL PHE ARG SEQRES 7 A 295 PHE GLY MET SER GLY SER PHE GLN LEU VAL PRO ARG GLU SEQRES 8 A 295 GLU LEU PRO ARG HIS ALA HIS LEU ARG PHE TYR THR ALA SEQRES 9 A 295 PRO PRO GLY PRO ARG LEU ALA LEU CYS PHE VAL ASP ILE SEQRES 10 A 295 ARG ARG PHE GLY ARG TRP ASP LEU GLY GLY LYS TRP GLN SEQRES 11 A 295 PRO GLY ARG GLY PRO CYS VAL LEU GLN GLU TYR GLN GLN SEQRES 12 A 295 PHE ARG GLU ASN VAL LEU ARG ASN LEU ALA ASP LYS ALA SEQRES 13 A 295 PHE ASP ARG PRO ILE CYS GLU ALA LEU LEU ASP GLN ARG SEQRES 14 A 295 PHE PHE ASN GLY ILE GLY ASN TYR LEU ARG ALA GLU ILE SEQRES 15 A 295 LEU TYR ARG LEU LYS ILE PRO PRO PHE GLU LYS ALA ARG SEQRES 16 A 295 SER VAL LEU GLU ALA LEU GLN GLN HIS ARG PRO SER PRO SEQRES 17 A 295 GLU LEU THR LEU SER GLN LYS ILE ARG THR LYS LEU GLN SEQRES 18 A 295 ASN PRO ASP LEU LEU GLU LEU CYS HIS SER VAL PRO LYS SEQRES 19 A 295 GLU VAL VAL GLN LEU GLY GLY LYS GLY TYR GLY SER GLU SEQRES 20 A 295 SER GLY GLU GLU ASP PHE ALA ALA PHE ARG ALA TRP LEU SEQRES 21 A 295 ARG CYS TYR GLY MET PRO GLY MET SER SER LEU GLN ASP SEQRES 22 A 295 ARG HIS GLY ARG THR ILE TRP PHE GLN GLY ASP PRO GLY SEQRES 23 A 295 PRO LEU ALA PRO LYS GLY ARG LYS SER SEQRES 1 B 13 DC DG DT DC DC DA 8Y9 DG DT DC DT DA DC SEQRES 1 C 13 DT DA DG DA DC DC DT DG DG DA DC DG DG SEQRES 1 D 295 MET GLY GLN GLY PRO GLU LEU HIS LEU ALA SER GLN PHE SEQRES 2 D 295 VAL ASN GLU ALA CYS ARG ALA LEU VAL PHE GLY GLY CYS SEQRES 3 D 295 VAL GLU LYS SER SER VAL SER ARG ASN PRO GLU VAL PRO SEQRES 4 D 295 PHE GLU SER SER ALA TYR ARG ILE SER ALA SER ALA ARG SEQRES 5 D 295 GLY LYS GLU LEU ARG LEU ILE LEU SER PRO LEU PRO GLY SEQRES 6 D 295 ALA GLN PRO GLN GLN GLU PRO LEU ALA LEU VAL PHE ARG SEQRES 7 D 295 PHE GLY MET SER GLY SER PHE GLN LEU VAL PRO ARG GLU SEQRES 8 D 295 GLU LEU PRO ARG HIS ALA HIS LEU ARG PHE TYR THR ALA SEQRES 9 D 295 PRO PRO GLY PRO ARG LEU ALA LEU CYS PHE VAL ASP ILE SEQRES 10 D 295 ARG ARG PHE GLY ARG TRP ASP LEU GLY GLY LYS TRP GLN SEQRES 11 D 295 PRO GLY ARG GLY PRO CYS VAL LEU GLN GLU TYR GLN GLN SEQRES 12 D 295 PHE ARG GLU ASN VAL LEU ARG ASN LEU ALA ASP LYS ALA SEQRES 13 D 295 PHE ASP ARG PRO ILE CYS GLU ALA LEU LEU ASP GLN ARG SEQRES 14 D 295 PHE PHE ASN GLY ILE GLY ASN TYR LEU ARG ALA GLU ILE SEQRES 15 D 295 LEU TYR ARG LEU LYS ILE PRO PRO PHE GLU LYS ALA ARG SEQRES 16 D 295 SER VAL LEU GLU ALA LEU GLN GLN HIS ARG PRO SER PRO SEQRES 17 D 295 GLU LEU THR LEU SER GLN LYS ILE ARG THR LYS LEU GLN SEQRES 18 D 295 ASN PRO ASP LEU LEU GLU LEU CYS HIS SER VAL PRO LYS SEQRES 19 D 295 GLU VAL VAL GLN LEU GLY GLY LYS GLY TYR GLY SER GLU SEQRES 20 D 295 SER GLY GLU GLU ASP PHE ALA ALA PHE ARG ALA TRP LEU SEQRES 21 D 295 ARG CYS TYR GLY MET PRO GLY MET SER SER LEU GLN ASP SEQRES 22 D 295 ARG HIS GLY ARG THR ILE TRP PHE GLN GLY ASP PRO GLY SEQRES 23 D 295 PRO LEU ALA PRO LYS GLY ARG LYS SER SEQRES 1 E 13 DC DG DT DC DC DA 8Y9 DG DT DC DT DA DC SEQRES 1 F 13 DT DA DG DA DC DC DT DG DG DA DC DG DG HET 8Y9 B 7 22 HET 8Y9 E 7 22 HETNAM 8Y9 [(2~{R},3~{S},5~{R})-5-[(5~{S})-5-CARBAMIMIDAMIDO-2,4- HETNAM 2 8Y9 BIS(OXIDANYLIDENE)IMIDAZOLIDIN-1-YL]-3-OXIDANYL- HETNAM 3 8Y9 OXOLAN-2-YL]METHY L DIHYDROGEN PHOSPHATE HETSYN 8Y9 (S)-GH FORMUL 2 8Y9 2(C9 H16 N5 O8 P) FORMUL 7 HOH *65(H2 O) HELIX 1 AA1 GLN A 3 CYS A 18 1 16 HELIX 2 AA2 GLU A 140 ARG A 150 1 11 HELIX 3 AA3 ASP A 154 ASP A 158 5 5 HELIX 4 AA4 PRO A 160 LEU A 165 1 6 HELIX 5 AA5 GLY A 175 LYS A 187 1 13 HELIX 6 AA6 LYS A 193 ALA A 200 1 8 HELIX 7 AA7 ASP A 224 GLY A 240 1 17 HELIX 8 AA8 PHE A 253 LEU A 260 1 8 HELIX 9 AA9 GLN D 3 CYS D 18 1 16 HELIX 10 AB1 GLU D 140 ARG D 150 1 11 HELIX 11 AB2 ASP D 154 ASP D 158 5 5 HELIX 12 AB3 PRO D 160 LEU D 165 1 6 HELIX 13 AB4 GLY D 175 LYS D 187 1 13 HELIX 14 AB5 LYS D 193 ALA D 200 1 8 HELIX 15 AB6 ASP D 224 GLY D 240 1 17 HELIX 16 AB7 GLY D 249 ASP D 252 5 4 HELIX 17 AB8 PHE D 253 LEU D 260 1 8 SHEET 1 AA1 8 SER A 84 PRO A 89 0 SHEET 2 AA1 8 LEU A 110 VAL A 115 -1 O CYS A 113 N GLN A 86 SHEET 3 AA1 8 ALA A 97 THR A 103 -1 N LEU A 99 O PHE A 114 SHEET 4 AA1 8 PHE A 23 LYS A 29 -1 N GLU A 28 O ARG A 100 SHEET 5 AA1 8 VAL A 38 ARG A 52 -1 O TYR A 45 N PHE A 23 SHEET 6 AA1 8 GLU A 55 PRO A 62 -1 O ARG A 57 N SER A 50 SHEET 7 AA1 8 LEU A 73 ARG A 78 -1 O PHE A 77 N LEU A 56 SHEET 8 AA1 8 ARG A 122 ASP A 124 -1 O ARG A 122 N ARG A 78 SHEET 1 AA2 2 SER A 269 GLN A 272 0 SHEET 2 AA2 2 THR A 278 PHE A 281 -1 O PHE A 281 N SER A 269 SHEET 1 AA3 8 SER D 84 PRO D 89 0 SHEET 2 AA3 8 LEU D 110 VAL D 115 -1 O CYS D 113 N GLN D 86 SHEET 3 AA3 8 ALA D 97 THR D 103 -1 N LEU D 99 O PHE D 114 SHEET 4 AA3 8 PHE D 23 LYS D 29 -1 N GLU D 28 O ARG D 100 SHEET 5 AA3 8 VAL D 38 ARG D 52 -1 O TYR D 45 N PHE D 23 SHEET 6 AA3 8 GLU D 55 PRO D 62 -1 O SER D 61 N ARG D 46 SHEET 7 AA3 8 LEU D 73 ARG D 78 -1 O PHE D 77 N LEU D 56 SHEET 8 AA3 8 ARG D 122 ASP D 124 -1 O ARG D 122 N ARG D 78 SHEET 1 AA4 2 SER D 269 GLN D 272 0 SHEET 2 AA4 2 THR D 278 PHE D 281 -1 O PHE D 281 N SER D 269 LINK O3' DA B 6 P 8Y9 B 7 1555 1555 1.61 LINK O3' 8Y9 B 7 P DG B 8 1555 1555 1.61 LINK O3' DA E 6 P 8Y9 E 7 1555 1555 1.60 LINK O3' 8Y9 E 7 P DG E 8 1555 1555 1.60 CISPEP 1 GLN A 67 PRO A 68 0 -2.59 CISPEP 2 GLN D 67 PRO D 68 0 4.87 CRYST1 88.604 142.564 71.074 90.00 90.00 90.00 P 21 21 2 8 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 0.011286 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007014 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014070 0.00000