PDB Short entry for 6HPH HEADER HYDROLASE 20-SEP-18 6HPH TITLE CRYSTAL STRUCTURE OF HUMAN PIF1 HELICASE IN COMPLEX WITH AMP-PNP 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 OTHER_DETAILS: SRM - ARTIFICIAL TAG 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PIF1, 5'-3' DNA HELICASE, DUPLEX UNWINDING, TELOMERE MAINTENANCE, DNA KEYWDS 2 REPAIR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.M.LEVDIKOV,S.DEHGHANI-TAFTI,B.D.BAX,C.M.SANDERS,A.A.ANTSON REVDAT 3 17-APR-19 6HPH 1 JRNL REVDAT 2 13-FEB-19 6HPH 1 JRNL REVDAT 1 23-JAN-19 6HPH 0 JRNL AUTH S.DEHGHANI-TAFTI,V.LEVDIKOV,A.A.ANTSON,B.BAX,C.M.SANDERS JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF THE NUCLEOTIDE AND DNA JRNL TITL 2 BINDING ACTIVITIES OF THE HUMAN PIF1 HELICASE. JRNL REF NUCLEIC ACIDS RES. V. 47 3208 2019 JRNL REFN ESSN 1362-4962 JRNL PMID 30698796 JRNL DOI 10.1093/NAR/GKZ028 REMARK 2 REMARK 2 RESOLUTION. 1.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 142572 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) : 0.129 REMARK 3 R VALUE (WORKING SET) : 0.127 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 7307 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) : 1.13 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 9436 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.3070 REMARK 3 BIN FREE R VALUE SET COUNT : 464 REMARK 3 BIN FREE R VALUE : 0.3250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3187 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 857 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.12000 REMARK 3 B22 (A**2) : 0.91000 REMARK 3 B33 (A**2) : -1.03000 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): 0.030 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.033 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.025 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.247 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.983 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.974 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3535 ; 0.029 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3501 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4829 ; 2.496 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8030 ; 1.604 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 478 ; 5.966 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 155 ;36.317 ;22.839 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 628 ;14.198 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;22.121 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 556 ; 0.165 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4097 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 850 ; 0.008 ; 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): 1778 ; 2.453 ; 1.596 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1777 ; 2.424 ; 1.595 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2237 ; 3.032 ; 2.411 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2238 ; 3.044 ; 2.411 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1753 ; 4.503 ; 2.017 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1754 ; 4.502 ; 2.017 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2568 ; 5.771 ; 2.888 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4817 ; 7.005 ;17.168 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4225 ; 5.888 ;14.686 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 7026 ; 6.577 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 184 ;44.717 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7632 ;15.715 ; 5.000 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 : 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 REMARK 4 REMARK 4 6HPH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1200012018. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-SEP-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 -8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 149927 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.130 REMARK 200 RESOLUTION RANGE LOW (A) : 49.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 6HPQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA-ACETATE, PEG 8K, PEG1K, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 38.82000 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 38.82000 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 36.64000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 71.64500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.64000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 71.64500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.82000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.64000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 71.64500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.82000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.64000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 71.64500 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: 970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 NE2 GLN A 589 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1293 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1565 LIES ON A SPECIAL POSITION. 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 CB GLN A 466 O HOH A 1039 1.95 REMARK 500 CD GLN A 542 O HOH A 903 2.07 REMARK 500 NH1 ARG A 491 O HOH A 901 2.11 REMARK 500 OG1 THR A 613 O HOH A 902 2.13 REMARK 500 SD MET A 453 O HOH A 1695 2.14 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 CE MET A 453 O HOH A 1005 4555 2.02 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 HIS A 269 NE2 HIS A 269 CD2 -0.068 REMARK 500 ASP A 595 CG ASP A 595 OD2 -0.157 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 VAL A 258 CA - CB - CG2 ANGL. DEV. = 9.6 DEGREES REMARK 500 CYS A 261 CA - CB - SG ANGL. DEV. = 14.3 DEGREES REMARK 500 ARG A 294 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 302 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 324 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 PHE A 387 CB - CG - CD1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 405 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 417 CG - CD - NE ANGL. DEV. = -16.7 DEGREES REMARK 500 ARG A 424 CB - CG - CD ANGL. DEV. = 20.1 DEGREES REMARK 500 ARG A 424 CD - NE - CZ ANGL. DEV. = 8.8 DEGREES REMARK 500 ARG A 424 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 424 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 LEU A 434 CA - CB - CG ANGL. DEV. = 22.2 DEGREES REMARK 500 GLU A 442 CA - CB - CG ANGL. DEV. = 16.9 DEGREES REMARK 500 ARG A 449 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 449 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 MET A 453 CG - SD - CE ANGL. DEV. = 18.0 DEGREES REMARK 500 ARG A 515 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 LEU A 517 CB - CG - CD1 ANGL. DEV. = 14.3 DEGREES REMARK 500 ARG A 528 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 528 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 592 NE - CZ - NH2 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 615 CA - CB - CG ANGL. DEV. = 16.5 DEGREES REMARK 500 ARG A 618 NE - CZ - NH1 ANGL. DEV. = 4.0 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 -141.79 -102.34 REMARK 500 ARG A 398 66.99 -113.16 REMARK 500 ASN A 456 88.38 -155.15 REMARK 500 ALA A 549 34.61 -149.81 REMARK 500 ASP A 563 18.93 -144.94 REMARK 500 CYS A 564 76.81 -155.51 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 A1722 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A1723 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A1724 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A1725 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A1726 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH A1727 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH A1728 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A1729 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A1730 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A1731 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A1732 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A1733 DISTANCE = 6.14 ANGSTROMS REMARK 525 HOH A1734 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH A1735 DISTANCE = 6.33 ANGSTROMS REMARK 525 HOH A1736 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH A1737 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH A1738 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH A1739 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH A1740 DISTANCE = 6.40 ANGSTROMS REMARK 525 HOH A1741 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH A1742 DISTANCE = 6.64 ANGSTROMS REMARK 525 HOH A1743 DISTANCE = 6.81 ANGSTROMS REMARK 525 HOH A1744 DISTANCE = 6.87 ANGSTROMS REMARK 525 HOH A1745 DISTANCE = 6.95 ANGSTROMS REMARK 525 HOH A1746 DISTANCE = 7.03 ANGSTROMS REMARK 525 HOH A1747 DISTANCE = 7.08 ANGSTROMS REMARK 525 HOH A1748 DISTANCE = 7.13 ANGSTROMS REMARK 525 HOH A1749 DISTANCE = 7.14 ANGSTROMS REMARK 525 HOH A1750 DISTANCE = 7.25 ANGSTROMS REMARK 525 HOH A1751 DISTANCE = 7.26 ANGSTROMS REMARK 525 HOH A1752 DISTANCE = 7.44 ANGSTROMS REMARK 525 HOH A1753 DISTANCE = 7.46 ANGSTROMS REMARK 525 HOH A1754 DISTANCE = 7.83 ANGSTROMS REMARK 525 HOH A1755 DISTANCE = 8.45 ANGSTROMS REMARK 525 HOH A1756 DISTANCE = 8.95 ANGSTROMS REMARK 525 HOH A1757 DISTANCE = 9.53 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 178.9 REMARK 620 3 ANP A 801 O1B 88.5 92.0 REMARK 620 4 HOH A1058 O 88.3 91.3 175.4 REMARK 620 5 HOH A1119 O 88.7 92.3 87.6 89.1 REMARK 620 6 HOH A1142 O 85.5 93.5 93.2 89.8 174.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ANP A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 802 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6HPQ RELATED DB: PDB REMARK 900 RELATED ID: 6HPT RELATED DB: PDB REMARK 900 RELATED ID: 6HPV RELATED DB: PDB DBREF 6HPH A 206 620 UNP Q9H611 PIF1_HUMAN 206 620 SEQADV 6HPH SER A 203 UNP Q9H611 EXPRESSION TAG SEQADV 6HPH ARG A 204 UNP Q9H611 EXPRESSION TAG SEQADV 6HPH 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 CYS 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 HET ANP A 801 31 HET MG A 802 1 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM MG MAGNESIUM ION FORMUL 2 ANP C10 H17 N6 O12 P3 FORMUL 3 MG MG 2+ FORMUL 4 HOH *857(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 CYS A 467 1 9 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 ILE A 339 N LEU A 303 SHEET 5 AA1 6 ILE A 224 GLY A 228 1 N ILE A 224 O ILE A 340 SHEET 6 AA1 6 VAL A 372 LEU A 376 1 O LEU A 376 N THR A 227 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 2.13 LINK O2G ANP A 801 MG MG A 802 1555 1555 2.04 LINK O1B ANP A 801 MG MG A 802 1555 1555 2.10 LINK MG MG A 802 O HOH A1058 1555 1555 2.07 LINK MG MG A 802 O HOH A1119 1555 1555 2.13 LINK MG MG A 802 O HOH A1142 1555 1555 2.10 SITE 1 AC1 30 MET A 205 GLN A 206 GLN A 211 ALA A 230 SITE 2 AC1 30 GLY A 231 THR A 232 GLY A 233 LYS A 234 SITE 3 AC1 30 SER A 235 TYR A 236 GLU A 307 GLN A 346 SITE 4 AC1 30 TRP A 380 ARG A 381 GLY A 559 ARG A 584 SITE 5 AC1 30 MG A 802 HOH A 924 HOH A 957 HOH A1058 SITE 6 AC1 30 HOH A1064 HOH A1095 HOH A1115 HOH A1119 SITE 7 AC1 30 HOH A1142 HOH A1177 HOH A1188 HOH A1214 SITE 8 AC1 30 HOH A1265 HOH A1281 SITE 1 AC2 5 SER A 235 ANP A 801 HOH A1058 HOH A1119 SITE 2 AC2 5 HOH A1142 CRYST1 73.280 143.290 77.640 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 0.013646 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006979 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012880 0.00000