HEADER DNA BINDING PROTEIN/DNA 17-MAR-16 5ITQ TITLE CRYSTAL STRUCTURE OF HUMAN NEIL1, FREE PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE 8-LIKE 1; COMPND 3 CHAIN: A; 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 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 KEYWDS DNA GLYCOSYLASE NEIL1 FPG NEI BASE EXCISION REPAIR, DNA BINDING KEYWDS 2 PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.ZHU,L.LU,J.ZHANG,Z.YUE,J.SONG,S.ZONG,M.LIU,O.STOVICEK,Y.GAO,C.YI REVDAT 3 08-NOV-23 5ITQ 1 JRNL REMARK REVDAT 2 03-AUG-16 5ITQ 1 JRNL REVDAT 1 06-JUL-16 5ITQ 0 JRNL AUTH C.ZHU,L.LU,J.ZHANG,Z.YUE,J.SONG,S.ZONG,M.LIU,O.STOVICEK, JRNL AUTH 2 Y.Q.GAO,C.YI JRNL TITL TAUTOMERIZATION-DEPENDENT RECOGNITION AND EXCISION OF JRNL TITL 2 OXIDATION DAMAGE IN BASE-EXCISION DNA REPAIR JRNL REF PROC.NATL.ACAD.SCI.USA V. 113 7792 2016 JRNL REFN ESSN 1091-6490 JRNL PMID 27354518 JRNL DOI 10.1073/PNAS.1604591113 REMARK 2 REMARK 2 RESOLUTION. 1.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 66.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 52390 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) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2795 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) : 1.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.52 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3865 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 221 REMARK 3 BIN FREE R VALUE : 0.2590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2265 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 465 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5ITQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219419. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-14 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 : BL17U 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 : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52396 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 66.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : 0.05500 REMARK 200 FOR THE DATA SET : 27.2700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.84000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.630 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: 1TDH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CACODYLIC ACID (PH 7.0), 0.1M REMARK 280 NACL, 0.05 M MGCL2, 24%(W/V) PEG 8000, PH 6.5, EVAPORATION, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 66.22700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.23618 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 16.93033 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 66.22700 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 38.23618 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 16.93033 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 66.22700 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 38.23618 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 16.93033 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 76.47235 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 33.86067 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 76.47235 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 33.86067 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 76.47235 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 33.86067 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 681 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 746 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 MET A 1 REMARK 465 HIS A 204 REMARK 465 ARG A 205 REMARK 465 PRO A 206 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 203 CG CD OE1 NE2 REMARK 470 SER A 207 OG 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 O HOH A 418 O HOH A 515 1.54 REMARK 500 NE2 GLN A 143 O HOH A 301 1.56 REMARK 500 O ASP A 124 O HOH A 302 1.74 REMARK 500 O HOH A 308 O HOH A 599 1.77 REMARK 500 O HOH A 349 O HOH A 362 1.84 REMARK 500 O HOH A 304 O HOH A 480 1.86 REMARK 500 O HOH A 425 O HOH A 586 1.91 REMARK 500 O HOH A 532 O HOH A 599 1.92 REMARK 500 NE ARG A 133 O HOH A 303 1.94 REMARK 500 O HOH A 340 O HOH A 609 1.94 REMARK 500 NE2 GLN A 142 O HOH A 304 1.94 REMARK 500 O HOH A 325 O HOH A 513 1.98 REMARK 500 NH1 ARG A 19 O HOH A 305 1.99 REMARK 500 O HOH A 343 O HOH A 418 2.00 REMARK 500 N SER A 207 O HOH A 306 2.01 REMARK 500 OE2 GLU A 146 O HOH A 304 2.05 REMARK 500 O HOH A 310 O HOH A 338 2.05 REMARK 500 O HOH A 712 O HOH A 730 2.06 REMARK 500 NH2 ARG A 57 O HOH A 307 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 402 O HOH A 542 2555 1.01 REMARK 500 O HOH A 442 O HOH A 536 2555 1.39 REMARK 500 O HOH A 461 O HOH A 556 6454 1.40 REMARK 500 O HOH A 429 O HOH A 673 2555 1.71 REMARK 500 O HOH A 503 O HOH A 545 9554 1.80 REMARK 500 O HOH A 322 O HOH A 539 3555 1.88 REMARK 500 O HOH A 376 O HOH A 429 3555 1.92 REMARK 500 O HOH A 581 O HOH A 723 8555 2.15 REMARK 500 O HOH A 636 O HOH A 730 8555 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 GLY A 127 CA GLY A 127 C -0.099 REMARK 500 ARG A 133 CD ARG A 133 NE -0.110 REMARK 500 SER A 147 CB SER A 147 OG 0.124 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 52 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 90 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 90 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 100 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 109 NE - CZ - NH1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG A 109 NE - CZ - NH2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG A 122 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 133 CG - CD - NE ANGL. DEV. = -13.2 DEGREES REMARK 500 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 8.9 DEGREES REMARK 500 ARG A 133 NE - CZ - NH2 ANGL. DEV. = -9.7 DEGREES REMARK 500 ASP A 154 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 179 NE - CZ - NH2 ANGL. DEV. = -3.1 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 PHE A 40 136.71 -172.26 REMARK 500 ALA A 44 106.41 -165.32 REMARK 500 PRO A 68 171.75 -48.56 REMARK 500 ASP A 116 89.72 -166.31 REMARK 500 GLU A 209 -76.17 -67.80 REMARK 500 SER A 246 -166.72 -108.72 REMARK 500 CYS A 262 -53.80 -133.45 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 GLN A 67 PRO A 68 -40.44 REMARK 500 PRO A 105 PRO A 106 45.56 REMARK 500 GLN A 202 GLN A 203 124.36 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 ARG A 133 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLN A 67 -12.82 REMARK 500 PRO A 105 11.54 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 762 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A 763 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A 764 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH A 765 DISTANCE = 6.51 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ITX RELATED DB: PDB REMARK 900 RELATED ID: 5ITY RELATED DB: PDB REMARK 900 RELATED ID: 5ITQ RELATED DB: PDB REMARK 900 RELATED ID: 5ITT RELATED DB: PDB REMARK 900 RELATED ID: 5ITU RELATED DB: PDB DBREF 5ITQ A 1 290 UNP Q96FI4 NEIL1_HUMAN 1 290 SEQADV 5ITQ SER A 147 UNP Q96FI4 ASN 147 ENGINEERED MUTATION SEQADV 5ITQ ARG A 242 UNP Q96FI4 LYS 242 ENGINEERED MUTATION SEQRES 1 A 290 MET PRO GLU GLY PRO GLU LEU HIS LEU ALA SER GLN PHE SEQRES 2 A 290 VAL ASN GLU ALA CYS ARG ALA LEU VAL PHE GLY GLY CYS SEQRES 3 A 290 VAL GLU LYS SER SER VAL SER ARG ASN PRO GLU VAL PRO SEQRES 4 A 290 PHE GLU SER SER ALA TYR ARG ILE SER ALA SER ALA ARG SEQRES 5 A 290 GLY LYS GLU LEU ARG LEU ILE LEU SER PRO LEU PRO GLY SEQRES 6 A 290 ALA GLN PRO GLN GLN GLU PRO LEU ALA LEU VAL PHE ARG SEQRES 7 A 290 PHE GLY MET SER GLY SER PHE GLN LEU VAL PRO ARG GLU SEQRES 8 A 290 GLU LEU PRO ARG HIS ALA HIS LEU ARG PHE TYR THR ALA SEQRES 9 A 290 PRO PRO GLY PRO ARG LEU ALA LEU CYS PHE VAL ASP ILE SEQRES 10 A 290 ARG ARG PHE GLY ARG TRP ASP LEU GLY GLY LYS TRP GLN SEQRES 11 A 290 PRO GLY ARG GLY PRO CYS VAL LEU GLN GLU TYR GLN GLN SEQRES 12 A 290 PHE ARG GLU SER VAL LEU ARG ASN LEU ALA ASP LYS ALA SEQRES 13 A 290 PHE ASP ARG PRO ILE CYS GLU ALA LEU LEU ASP GLN ARG SEQRES 14 A 290 PHE PHE ASN GLY ILE GLY ASN TYR LEU ARG ALA GLU ILE SEQRES 15 A 290 LEU TYR ARG LEU LYS ILE PRO PRO PHE GLU LYS ALA ARG SEQRES 16 A 290 SER VAL LEU GLU ALA LEU GLN GLN HIS ARG PRO SER PRO SEQRES 17 A 290 GLU LEU THR LEU SER GLN LYS ILE ARG THR LYS LEU GLN SEQRES 18 A 290 ASN PRO ASP LEU LEU GLU LEU CYS HIS SER VAL PRO LYS SEQRES 19 A 290 GLU VAL VAL GLN LEU GLY GLY ARG GLY TYR GLY SER GLU SEQRES 20 A 290 SER GLY GLU GLU ASP PHE ALA ALA PHE ARG ALA TRP LEU SEQRES 21 A 290 ARG CYS TYR GLY MET PRO GLY MET SER SER LEU GLN ASP SEQRES 22 A 290 ARG HIS GLY ARG THR ILE TRP PHE GLN GLY ASP PRO GLY SEQRES 23 A 290 PRO LEU ALA PRO FORMUL 2 HOH *465(H2 O) HELIX 1 AA1 GLU A 3 ARG A 19 1 17 HELIX 2 AA2 GLU A 91 LEU A 93 5 3 HELIX 3 AA3 GLU A 140 ASN A 151 1 12 HELIX 4 AA4 ASP A 154 ARG A 159 5 6 HELIX 5 AA5 PRO A 160 LEU A 165 1 6 HELIX 6 AA6 GLY A 175 LYS A 187 1 13 HELIX 7 AA7 LYS A 193 GLU A 199 1 7 HELIX 8 AA8 ALA A 200 GLN A 202 5 3 HELIX 9 AA9 THR A 211 LYS A 219 1 9 HELIX 10 AB1 ASP A 224 GLY A 241 1 18 HELIX 11 AB2 SER A 248 LEU A 260 1 13 SHEET 1 AA1 5 PHE A 23 CYS A 26 0 SHEET 2 AA1 5 GLU A 41 ARG A 52 -1 O TYR A 45 N PHE A 23 SHEET 3 AA1 5 GLU A 55 PRO A 62 -1 O ARG A 57 N SER A 50 SHEET 4 AA1 5 LEU A 73 ARG A 78 -1 O PHE A 77 N LEU A 56 SHEET 5 AA1 5 ARG A 122 LEU A 125 -1 O ARG A 122 N ARG A 78 SHEET 1 AA2 4 GLU A 28 LYS A 29 0 SHEET 2 AA2 4 ALA A 97 TYR A 102 -1 O ARG A 100 N GLU A 28 SHEET 3 AA2 4 LEU A 110 ASP A 116 -1 O PHE A 114 N LEU A 99 SHEET 4 AA2 4 GLY A 83 PRO A 89 -1 N GLN A 86 O CYS A 113 SHEET 1 AA3 2 SER A 269 GLN A 272 0 SHEET 2 AA3 2 THR A 278 PHE A 281 -1 O ILE A 279 N LEU A 271 CRYST1 132.454 132.454 50.791 90.00 90.00 120.00 H 3 9 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 0.007550 0.004359 0.000000 0.00000 SCALE2 0.000000 0.008718 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019689 0.00000