HEADER DNA BINDING PROTEIN 28-MAY-24 9FI9 TITLE HUMAN PIF + Z48847594 (OCCUPANCY 0.7) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT DNA HELICASE PIF1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DNA REPAIR AND RECOMBINATION HELICASE PIF1,PIF1/RRM3 DNA COMPND 5 HELICASE-LIKE PROTEIN; COMPND 6 EC: 3.6.4.12; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: THE ELECTRON DENSITY MAP SUGGESTED CYS 426 WAS COMPND 10 OXIDISED SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PIF1, C15ORF20; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HELICASE, INHIBITOR, COMPLEX, AMPPNP, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.D.BAX,C.M.SANDERS,A.A.ANTSON,J.BRANDAO-NETO REVDAT 2 30-OCT-24 9FI9 1 JRNL REVDAT 1 02-OCT-24 9FI9 0 JRNL AUTH M.J.A.WEVER,F.R.SCOMMEGNA,S.EGEA-RODRIGUEZ,S.DEHGHANI-TAFTI, JRNL AUTH 2 J.BRANDAO-NETO,J.F.POISSON,I.HELFRICH,A.A.ANTSON, JRNL AUTH 3 V.RODESCHINI,B.BAX,D.ROCHE,C.M.SANDERS JRNL TITL STRUCTURE-BASED DISCOVERY OF FIRST INHIBITORS TARGETING THE JRNL TITL 2 HELICASE ACTIVITY OF HUMAN PIF1. JRNL REF NUCLEIC ACIDS RES. 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 39417423 JRNL DOI 10.1093/NAR/GKAE897 REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0419 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 43195 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 2134 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) : 1.73 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2888 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.12 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 159 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3185 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 614 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.31700 REMARK 3 B22 (A**2) : 1.10200 REMARK 3 B33 (A**2) : 1.21400 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): 0.115 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.111 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.089 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.982 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3784 ; 0.009 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5188 ; 1.810 ; 1.836 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 517 ; 6.064 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 52 ; 8.880 ; 5.865 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 680 ;14.436 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 578 ; 0.119 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2944 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1740 ; 0.230 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2406 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 512 ; 0.242 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.259 ; 0.200 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): 1894 ; 2.128 ; 2.380 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2428 ; 3.015 ; 4.264 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1890 ; 3.347 ; 2.789 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2745 ; 5.068 ; 4.947 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 : 3 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 : Ap 207 Ap 379 REMARK 3 ORIGIN FOR THE GROUP (A): -6.2287 -23.3837 1.6170 REMARK 3 T TENSOR REMARK 3 T11: 0.0407 T22: 0.0294 REMARK 3 T33: 0.0351 T12: 0.0033 REMARK 3 T13: 0.0115 T23: 0.0047 REMARK 3 L TENSOR REMARK 3 L11: 0.5370 L22: 0.0919 REMARK 3 L33: 0.2647 L12: 0.0308 REMARK 3 L13: -0.0460 L23: -0.1045 REMARK 3 S TENSOR REMARK 3 S11: 0.0022 S12: -0.0424 S13: 0.0145 REMARK 3 S21: -0.0094 S22: -0.0074 S23: 0.0100 REMARK 3 S31: 0.0033 S32: 0.0105 S33: 0.0053 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : Ap 382 Ap 435 REMARK 3 RESIDUE RANGE : Ap 552 Ap 602 REMARK 3 ORIGIN FOR THE GROUP (A): -23.2301 -24.1131 -20.7560 REMARK 3 T TENSOR REMARK 3 T11: 0.0452 T22: 0.0319 REMARK 3 T33: 0.0557 T12: -0.0040 REMARK 3 T13: -0.0021 T23: -0.0151 REMARK 3 L TENSOR REMARK 3 L11: 0.0886 L22: 0.3216 REMARK 3 L33: 0.3269 L12: 0.1641 REMARK 3 L13: -0.0730 L23: -0.1286 REMARK 3 S TENSOR REMARK 3 S11: -0.0048 S12: -0.0202 S13: 0.0049 REMARK 3 S21: -0.0378 S22: -0.0241 S23: 0.0089 REMARK 3 S31: 0.0134 S32: -0.0076 S33: 0.0289 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 : Ap 440 Ap 548 REMARK 3 ORIGIN FOR THE GROUP (A): -16.6339 -0.1000 -15.4893 REMARK 3 T TENSOR REMARK 3 T11: 0.0635 T22: 0.0092 REMARK 3 T33: 0.0574 T12: 0.0198 REMARK 3 T13: -0.0032 T23: -0.0096 REMARK 3 L TENSOR REMARK 3 L11: 0.2580 L22: 0.9768 REMARK 3 L33: 0.8005 L12: 0.0969 REMARK 3 L13: 0.4452 L23: 0.3300 REMARK 3 S TENSOR REMARK 3 S11: -0.0764 S12: -0.0215 S13: 0.0646 REMARK 3 S21: -0.0724 S22: -0.0458 S23: 0.0192 REMARK 3 S31: -0.1292 S32: -0.0423 S33: 0.1221 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 NOT BEEN USED REMARK 4 REMARK 4 9FI9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1292138973. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-18 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 : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91587 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43220 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.727 REMARK 200 RESOLUTION RANGE LOW (A) : 27.849 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: XCHEM 0.045ULS COMPOUND (0.5M) IN DMSO REMARK 280 ECHO DISPENSED INTO CRYSTAL DROP DROP = 0.3ULS PROTEIN + 0.3ULS REMARK 280 WELL +0.001ULS SEEDS. PROTEIN = 25ULS 30MGS/ML HUMAN PIF1 (206- REMARK 280 620) IN 10MM TRIS PH 7.5, 175MM NACL, 2%GLYCEROL, 5MM DTT, 0.1MM REMARK 280 PMSF + 21ULS 10MM TRIS, 2.7ULS 0.2M MGCL2, 5ULS 100MM AMPPNP + REMARK 280 27ULS H2O. WELL = 4% GLYCEROL, 27% PEG 2KMME, 0.1M NAACETATE, REMARK 280 0.1M TRIS PH8.5. SET UP ON DOUGLAS INSTRUMENTS ROBOT - TRAY ON REMARK 280 ICE - SET-UP ROOM TEMPERATURE - CRYSTALLISED 4 DEGREES C., VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 38.61900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.61900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 36.80000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 71.85700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.80000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 71.85700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.61900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.80000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 71.85700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.61900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.80000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 71.85700 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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 901 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1249 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1487 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1493 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1500 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1504 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1505 LIES ON A SPECIAL POSITION. 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 414 CD CE NZ 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 1020 O HOH A 1325 1.80 REMARK 500 O HOH A 1186 O HOH A 1405 1.86 REMARK 500 NE ARG A 618 O HOH A 902 1.93 REMARK 500 O HOH A 1274 O HOH A 1320 1.93 REMARK 500 O HOH A 1150 O HOH A 1349 1.96 REMARK 500 O HOH A 1405 O HOH A 1432 2.02 REMARK 500 O HOH A 1225 O HOH A 1462 2.06 REMARK 500 O HOH A 1100 O HOH A 1379 2.08 REMARK 500 O HOH A 1235 O HOH A 1313 2.09 REMARK 500 O HOH A 1310 O HOH A 1492 2.12 REMARK 500 NE2 GLN A 283 O HOH A 903 2.14 REMARK 500 O HOH A 1214 O HOH A 1424 2.14 REMARK 500 O HOH A 1286 O HOH A 1327 2.14 REMARK 500 O HOH A 907 O HOH A 1345 2.16 REMARK 500 O HOH A 1486 O HOH A 1510 2.17 REMARK 500 O HOH A 952 O HOH A 1061 2.18 REMARK 500 O HOH A 1334 O HOH A 1425 2.19 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 1184 O HOH A 1384 3555 1.83 REMARK 500 O HOH A 1344 O HOH A 1384 8445 2.06 REMARK 500 O HOH A 1362 O HOH A 1479 4555 2.07 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 405 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 405 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 CYS A 603 CB - CA - C ANGL. DEV. = -17.0 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 GLN A 346 -137.32 -97.61 REMARK 500 ARG A 398 68.27 -114.09 REMARK 500 ARG A 417 -162.27 -110.68 REMARK 500 ARG A 417 130.41 174.69 REMARK 500 ASP A 418 105.87 -57.23 REMARK 500 ASP A 418 70.38 48.55 REMARK 500 SER A 488 101.81 -163.15 REMARK 500 ALA A 533 -159.04 -90.97 REMARK 500 ALA A 533 -159.04 -92.25 REMARK 500 ALA A 549 31.21 -145.98 REMARK 500 CYS A 564 80.87 -157.50 REMARK 500 CYS A 564 82.20 -157.50 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 240 0.09 SIDE CHAIN 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 A1514 DISTANCE = 5.85 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 MG A 802 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 235 OG REMARK 620 2 ANP A 801 O2G 175.0 REMARK 620 3 ANP A 801 O1B 89.1 94.5 REMARK 620 4 HOH A 981 O 86.0 90.5 175.0 REMARK 620 5 HOH A1112 O 89.4 94.4 87.3 92.1 REMARK 620 6 HOH A1131 O 85.4 90.8 93.8 86.4 174.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 804 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 464 O REMARK 620 2 CYS A 467 O 80.2 REMARK 620 3 O0J A 803 O 90.6 77.7 REMARK 620 4 HOH A1054 O 72.8 109.3 40.1 REMARK 620 5 HOH A1088 O 163.6 112.9 83.1 93.0 REMARK 620 6 HOH A1194 O 102.2 81.0 152.9 167.0 89.9 REMARK 620 7 HOH A1194 O 100.8 79.9 152.7 167.1 91.5 1.7 REMARK 620 8 HOH A1300 O 94.2 154.9 77.9 46.2 69.8 124.0 125.2 REMARK 620 9 HOH A1337 O 164.5 101.6 104.8 120.1 27.1 63.3 64.8 90.4 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6HPH RELATED DB: PDB REMARK 900 1.13A AMPPNP COMPLEX DBREF 9FI9 A 206 620 UNP Q9H611 PIF1_HUMAN 206 620 SEQADV 9FI9 SER A 203 UNP Q9H611 EXPRESSION TAG SEQADV 9FI9 ARG A 204 UNP Q9H611 EXPRESSION TAG SEQADV 9FI9 MET A 205 UNP Q9H611 EXPRESSION TAG SEQRES 1 A 418 SER ARG MET GLN LEU SER GLU GLU GLN ALA ALA VAL LEU SEQRES 2 A 418 ARG ALA VAL LEU LYS GLY GLN SER ILE PHE PHE THR GLY SEQRES 3 A 418 SER ALA GLY THR GLY LYS SER TYR LEU LEU LYS ARG ILE SEQRES 4 A 418 LEU GLY SER LEU PRO PRO THR GLY THR VAL ALA THR ALA SEQRES 5 A 418 SER THR GLY VAL ALA ALA CYS HIS ILE GLY GLY THR THR SEQRES 6 A 418 LEU HIS ALA PHE ALA GLY ILE GLY SER GLY GLN ALA PRO SEQRES 7 A 418 LEU ALA GLN CYS VAL ALA LEU ALA GLN ARG PRO GLY VAL SEQRES 8 A 418 ARG GLN GLY TRP LEU ASN CYS GLN ARG LEU VAL ILE ASP SEQRES 9 A 418 GLU ILE SER MET VAL GLU ALA ASP LEU PHE ASP LYS LEU SEQRES 10 A 418 GLU ALA VAL ALA ARG ALA VAL ARG GLN GLN ASN LYS PRO SEQRES 11 A 418 PHE GLY GLY ILE GLN LEU ILE ILE CYS GLY ASP PHE LEU SEQRES 12 A 418 GLN LEU PRO PRO VAL THR LYS GLY SER GLN PRO PRO ARG SEQRES 13 A 418 PHE CYS PHE GLN SER LYS SER TRP LYS ARG CYS VAL PRO SEQRES 14 A 418 VAL THR LEU GLU LEU THR LYS VAL TRP ARG GLN ALA ASP SEQRES 15 A 418 GLN THR PHE ILE SER LEU LEU GLN ALA VAL ARG LEU GLY SEQRES 16 A 418 ARG CYS SER ASP GLU VAL THR ARG GLN LEU GLN ALA THR SEQRES 17 A 418 ALA SER HIS LYS VAL GLY ARG ASP GLY ILE VAL ALA THR SEQRES 18 A 418 ARG LEU CSO THR HIS GLN ASP ASP VAL ALA LEU THR ASN SEQRES 19 A 418 GLU ARG ARG LEU GLN GLU LEU PRO GLY LYS VAL HIS ARG SEQRES 20 A 418 PHE GLU ALA MET ASP SER ASN PRO GLU LEU ALA SER THR SEQRES 21 A 418 LEU ASP ALA GLN CYS PRO VAL SER GLN LEU LEU GLN LEU SEQRES 22 A 418 LYS LEU GLY ALA GLN VAL MET LEU VAL LYS ASN LEU SER SEQRES 23 A 418 VAL SER ARG GLY LEU VAL ASN GLY ALA ARG GLY VAL VAL SEQRES 24 A 418 VAL GLY PHE GLU ALA GLU GLY ARG GLY LEU PRO GLN VAL SEQRES 25 A 418 ARG PHE LEU CYS GLY VAL THR GLU VAL ILE HIS ALA ASP SEQRES 26 A 418 ARG TRP THR VAL GLN ALA THR GLY GLY GLN LEU LEU SER SEQRES 27 A 418 ARG GLN GLN LEU PRO LEU GLN LEU ALA TRP ALA MET SER SEQRES 28 A 418 ILE HIS LYS SER GLN GLY MET THR LEU ASP CYS VAL GLU SEQRES 29 A 418 ILE SER LEU GLY ARG VAL PHE ALA SER GLY GLN ALA TYR SEQRES 30 A 418 VAL ALA LEU SER ARG ALA ARG SER LEU GLN GLY LEU ARG SEQRES 31 A 418 VAL LEU ASP PHE ASP PRO MET ALA VAL ARG CYS ASP PRO SEQRES 32 A 418 ARG VAL LEU HIS PHE TYR ALA THR LEU ARG ARG GLY ARG SEQRES 33 A 418 SER LEU MODRES 9FI9 CSO A 426 CYS MODIFIED RESIDUE HET CSO A 426 7 HET ANP A 801 31 HET MG A 802 1 HET O0J A 803 16 HET NA A 804 1 HETNAM CSO S-HYDROXYCYSTEINE HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM O0J N-[4-(2-AMINO-1,3-THIAZOL-4-YL)PHENYL]ACETAMIDE HETNAM NA SODIUM ION FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 ANP C10 H17 N6 O12 P3 FORMUL 3 MG MG 2+ FORMUL 4 O0J C11 H11 N3 O S FORMUL 5 NA NA 1+ FORMUL 6 HOH *614(H2 O) HELIX 1 AA1 SER A 208 LYS A 220 1 13 HELIX 2 AA2 GLY A 233 LEU A 245 1 13 HELIX 3 AA3 THR A 256 ILE A 263 1 8 HELIX 4 AA4 LEU A 268 GLY A 273 1 6 HELIX 5 AA5 PRO A 280 GLN A 289 1 10 HELIX 6 AA6 GLY A 292 CYS A 300 1 9 HELIX 7 AA7 GLU A 307 VAL A 311 5 5 HELIX 8 AA8 GLU A 312 GLN A 328 1 17 HELIX 9 AA9 LYS A 331 ILE A 336 5 6 HELIX 10 AB1 PHE A 359 SER A 363 5 5 HELIX 11 AB2 SER A 365 VAL A 370 1 6 HELIX 12 AB3 ASP A 384 LEU A 396 1 13 HELIX 13 AB4 SER A 400 THR A 410 1 11 HELIX 14 AB5 ALA A 411 HIS A 413 5 3 HELIX 15 AB6 HIS A 428 GLU A 442 1 15 HELIX 16 AB7 ASN A 456 GLU A 458 5 3 HELIX 17 AB8 LEU A 459 ALA A 465 1 7 HELIX 18 AB9 THR A 534 GLY A 536 5 3 HELIX 19 AC1 HIS A 555 GLN A 558 5 4 HELIX 20 AC2 GLY A 576 ARG A 584 1 9 HELIX 21 AC3 SER A 587 GLN A 589 5 3 HELIX 22 AC4 ASP A 597 VAL A 601 5 5 HELIX 23 AC5 ASP A 604 ARG A 615 1 12 SHEET 1 AA1 6 THR A 266 THR A 267 0 SHEET 2 AA1 6 THR A 250 ALA A 254 1 N ALA A 252 O THR A 266 SHEET 3 AA1 6 ARG A 302 ASP A 306 1 O VAL A 304 N VAL A 251 SHEET 4 AA1 6 GLN A 337 GLY A 342 1 O GLN A 337 N LEU A 303 SHEET 5 AA1 6 ILE A 224 THR A 227 1 N ILE A 224 O ILE A 340 SHEET 6 AA1 6 VAL A 372 GLU A 375 1 O VAL A 372 N PHE A 225 SHEET 1 AA2 4 ALA A 551 SER A 553 0 SHEET 2 AA2 4 THR A 423 CSO A 426 1 N CSO A 426 O MET A 552 SHEET 3 AA2 4 VAL A 565 SER A 568 1 O GLU A 566 N LEU A 425 SHEET 4 AA2 4 LEU A 591 LEU A 594 1 O LEU A 594 N ILE A 567 SHEET 1 AA3 2 HIS A 448 GLU A 451 0 SHEET 2 AA3 2 LEU A 472 LEU A 475 -1 O LEU A 473 N PHE A 450 SHEET 1 AA4 3 MET A 453 ASP A 454 0 SHEET 2 AA4 3 LEU A 538 GLN A 543 -1 O GLN A 542 N MET A 453 SHEET 3 AA4 3 ASP A 527 GLN A 532 -1 N VAL A 531 O LEU A 539 SHEET 1 AA5 5 THR A 521 VAL A 523 0 SHEET 2 AA5 5 PRO A 512 PHE A 516 -1 N VAL A 514 O GLU A 522 SHEET 3 AA5 5 ARG A 498 PHE A 504 -1 N GLY A 503 O GLN A 513 SHEET 4 AA5 5 GLN A 480 LEU A 483 -1 N VAL A 481 O GLY A 499 SHEET 5 AA5 5 LEU A 546 LEU A 548 -1 O GLN A 547 N MET A 482 LINK C LEU A 425 N CSO A 426 1555 1555 1.34 LINK C CSO A 426 N THR A 427 1555 1555 1.33 LINK OG SER A 235 MG MG A 802 1555 1555 2.19 LINK O ASP A 464 NA NA A 804 1555 1555 2.55 LINK O CYS A 467 NA NA A 804 1555 1555 2.60 LINK O2G ANP A 801 MG MG A 802 1555 1555 2.03 LINK O1B ANP A 801 MG MG A 802 1555 1555 2.17 LINK MG MG A 802 O HOH A 981 1555 1555 2.22 LINK MG MG A 802 O HOH A1112 1555 1555 2.09 LINK MG MG A 802 O HOH A1131 1555 1555 2.22 LINK O AO0J A 803 NA NA A 804 1555 1555 2.76 LINK NA NA A 804 O BHOH A1054 1555 1555 1.99 LINK NA NA A 804 O BHOH A1088 1555 1555 2.76 LINK NA NA A 804 O AHOH A1194 1555 1555 2.15 LINK NA NA A 804 O BHOH A1194 1555 1555 2.49 LINK NA NA A 804 O BHOH A1300 1555 1555 2.40 LINK NA NA A 804 O BHOH A1337 1555 1555 3.03 CRYST1 73.600 143.714 77.238 90.00 90.00 90.00 C 2 2 21 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 0.013587 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006958 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012947 0.00000