HEADER DNA BINDING PROTEIN 12-MAY-24 9FB8 TITLE XCHEM REFINED PIF1-X0076 COMPLEX 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 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, XCHEM, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.D.BAX,A.A.ANTSON,C.M.SANDERS,J.BRANDAO-NETO REVDAT 1 18-SEP-24 9FB8 0 JRNL AUTH C.M.SANDERS,B.D.BAX JRNL TITL STRUCTURE-BASED DISCOVERY OF FIRST ON-TARGET INHIBITORS OF JRNL TITL 2 THE HUMAN PIF1 HELICASE JRNL REF TO BE PUBLISHED JRNL REFN 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) : 27.83 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) : 0.173 REMARK 3 FREE R VALUE : 0.211 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 : NULL 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) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 159 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3150 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 373 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.20800 REMARK 3 B22 (A**2) : 0.90300 REMARK 3 B33 (A**2) : 1.30400 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): 0.114 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.111 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.090 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.891 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3362 ; 0.009 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4578 ; 1.896 ; 1.817 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 438 ; 5.641 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 44 ; 9.591 ; 6.364 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 558 ;13.335 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 526 ; 0.122 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2548 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1466 ; 0.230 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2256 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 287 ; 0.189 ; 0.200 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): 1710 ; 2.479 ; 2.731 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2150 ; 3.331 ; 4.899 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1652 ; 4.131 ; 3.170 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2424 ; 6.015 ; 5.622 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 : 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 9FB8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1292138517. 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) : 27.830 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 : NULL 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 (%): 45.11 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 + 0.3US 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL 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 A1257 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1263 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 SER A 203 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 ARG A 204 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 283 CD OE1 NE2 REMARK 470 LYS A 331 CE NZ REMARK 470 LYS A 414 CG CD CE NZ REMARK 470 ARG A 417 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 446 CG CD CE NZ REMARK 470 ARG A 602 CG CD NE CZ NH1 NH2 REMARK 470 SER A 621 CA C O CB 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 1139 O HOH A 1236 1.79 REMARK 500 O HOH A 1149 O HOH A 1179 1.86 REMARK 500 O HOH A 938 O HOH A 1079 1.90 REMARK 500 C O0J A 804 O HOH A 901 2.02 REMARK 500 C1 O0J A 804 O HOH A 901 2.03 REMARK 500 O HOH A 1222 O HOH A 1223 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 1037 O HOH A 1037 4555 1.85 REMARK 500 O HOH A 1202 O HOH A 1236 6444 1.98 REMARK 500 O HOH A 1112 O HOH A 1112 3454 2.18 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. = 3.4 DEGREES REMARK 500 ARG A 405 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 MET A 453 CG - SD - CE ANGL. DEV. = 11.5 DEGREES REMARK 500 ARG A 571 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 592 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 CYS A 603 CB - CA - C ANGL. DEV. = -14.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN A 346 -137.50 -98.64 REMARK 500 ARG A 398 68.42 -113.57 REMARK 500 ALA A 533 -159.66 -88.63 REMARK 500 ASP A 563 20.11 -143.08 REMARK 500 CYS A 564 82.47 -154.35 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 A1272 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A1273 DISTANCE = 6.57 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 O1G 175.1 REMARK 620 3 ANP A 801 O1B 89.2 94.5 REMARK 620 4 HOH A 942 O 86.7 89.5 175.9 REMARK 620 5 HOH A1062 O 89.3 94.0 88.1 92.7 REMARK 620 6 HOH A1080 O 86.6 90.0 93.5 85.5 175.5 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6HPH RELATED DB: PDB DBREF 9FB8 A 206 621 UNP Q9H611 PIF1_HUMAN 206 621 SEQADV 9FB8 SER A 203 UNP Q9H611 EXPRESSION TAG SEQADV 9FB8 ARG A 204 UNP Q9H611 EXPRESSION TAG SEQADV 9FB8 MET A 205 UNP Q9H611 EXPRESSION TAG SEQRES 1 A 419 SER ARG MET GLN LEU SER GLU GLU GLN ALA ALA VAL LEU SEQRES 2 A 419 ARG ALA VAL LEU LYS GLY GLN SER ILE PHE PHE THR GLY SEQRES 3 A 419 SER ALA GLY THR GLY LYS SER TYR LEU LEU LYS ARG ILE SEQRES 4 A 419 LEU GLY SER LEU PRO PRO THR GLY THR VAL ALA THR ALA SEQRES 5 A 419 SER THR GLY VAL ALA ALA CYS HIS ILE GLY GLY THR THR SEQRES 6 A 419 LEU HIS ALA PHE ALA GLY ILE GLY SER GLY GLN ALA PRO SEQRES 7 A 419 LEU ALA GLN CYS VAL ALA LEU ALA GLN ARG PRO GLY VAL SEQRES 8 A 419 ARG GLN GLY TRP LEU ASN CYS GLN ARG LEU VAL ILE ASP SEQRES 9 A 419 GLU ILE SER MET VAL GLU ALA ASP LEU PHE ASP LYS LEU SEQRES 10 A 419 GLU ALA VAL ALA ARG ALA VAL ARG GLN GLN ASN LYS PRO SEQRES 11 A 419 PHE GLY GLY ILE GLN LEU ILE ILE CYS GLY ASP PHE LEU SEQRES 12 A 419 GLN LEU PRO PRO VAL THR LYS GLY SER GLN PRO PRO ARG SEQRES 13 A 419 PHE CYS PHE GLN SER LYS SER TRP LYS ARG CYS VAL PRO SEQRES 14 A 419 VAL THR LEU GLU LEU THR LYS VAL TRP ARG GLN ALA ASP SEQRES 15 A 419 GLN THR PHE ILE SER LEU LEU GLN ALA VAL ARG LEU GLY SEQRES 16 A 419 ARG CYS SER ASP GLU VAL THR ARG GLN LEU GLN ALA THR SEQRES 17 A 419 ALA SER HIS LYS VAL GLY ARG ASP GLY ILE VAL ALA THR SEQRES 18 A 419 ARG LEU CYS THR HIS GLN ASP ASP VAL ALA LEU THR ASN SEQRES 19 A 419 GLU ARG ARG LEU GLN GLU LEU PRO GLY LYS VAL HIS ARG SEQRES 20 A 419 PHE GLU ALA MET ASP SER ASN PRO GLU LEU ALA SER THR SEQRES 21 A 419 LEU ASP ALA GLN CYS PRO VAL SER GLN LEU LEU GLN LEU SEQRES 22 A 419 LYS LEU GLY ALA GLN VAL MET LEU VAL LYS ASN LEU SER SEQRES 23 A 419 VAL SER ARG GLY LEU VAL ASN GLY ALA ARG GLY VAL VAL SEQRES 24 A 419 VAL GLY PHE GLU ALA GLU GLY ARG GLY LEU PRO GLN VAL SEQRES 25 A 419 ARG PHE LEU CYS GLY VAL THR GLU VAL ILE HIS ALA ASP SEQRES 26 A 419 ARG TRP THR VAL GLN ALA THR GLY GLY GLN LEU LEU SER SEQRES 27 A 419 ARG GLN GLN LEU PRO LEU GLN LEU ALA TRP ALA MET SER SEQRES 28 A 419 ILE HIS LYS SER GLN GLY MET THR LEU ASP CYS VAL GLU SEQRES 29 A 419 ILE SER LEU GLY ARG VAL PHE ALA SER GLY GLN ALA TYR SEQRES 30 A 419 VAL ALA LEU SER ARG ALA ARG SER LEU GLN GLY LEU ARG SEQRES 31 A 419 VAL LEU ASP PHE ASP PRO MET ALA VAL ARG CYS ASP PRO SEQRES 32 A 419 ARG VAL LEU HIS PHE TYR ALA THR LEU ARG ARG GLY ARG SEQRES 33 A 419 SER LEU SER HET ANP A 801 31 HET MG A 802 1 HET O0J A 803 16 HET O0J A 804 16 HET DMS A 805 4 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM O0J N-[4-(2-AMINO-1,3-THIAZOL-4-YL)PHENYL]ACETAMIDE HETNAM DMS DIMETHYL SULFOXIDE FORMUL 2 ANP C10 H17 N6 O12 P3 FORMUL 3 MG MG 2+ FORMUL 4 O0J 2(C11 H11 N3 O S) FORMUL 6 DMS C2 H6 O S FORMUL 7 HOH *373(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 LEU A 443 1 16 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 CYS A 426 1 N CYS 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 475 N HIS A 448 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 OG SER A 235 MG MG A 802 1555 1555 2.17 LINK O1G ANP A 801 MG MG A 802 1555 1555 2.03 LINK O1B ANP A 801 MG MG A 802 1555 1555 2.15 LINK MG MG A 802 O HOH A 942 1555 1555 2.21 LINK MG MG A 802 O HOH A1062 1555 1555 2.05 LINK MG MG A 802 O HOH A1080 1555 1555 2.21 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