HEADER HYDROLASE 29-MAR-17 5XDR TITLE CRYSTAL STRUCTURE OF HUMAN DEAH-BOX RNA HELICASE DHX15 IN COMPLEX WITH TITLE 2 ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRE-MRNA-SPLICING FACTOR ATP-DEPENDENT RNA HELICASE DHX15; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 110-795; COMPND 5 SYNONYM: ATP-DEPENDENT RNA HELICASE #46,DEAH BOX PROTEIN 15; COMPND 6 EC: 3.6.4.13; COMPND 7 ENGINEERED: YES; COMPND 8 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: DHX15, DBP1, DDX15; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS RNA HELICASE, DEAH-BOX, DHX15, PRP43, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.MURAKAMI,K.NAKANO,T.SHIMIZU,U.OHTO REVDAT 2 27-MAR-24 5XDR 1 SOURCE REVDAT 1 21-JUN-17 5XDR 0 JRNL AUTH K.MURAKAMI,K.NAKANO,T.SHIMIZU,U.OHTO JRNL TITL THE CRYSTAL STRUCTURE OF HUMAN DEAH-BOX RNA HELICASE 15 JRNL TITL 2 REVEALS A DOMAIN ORGANIZATION OF THE MAMMALIAN DEAH/RHA JRNL TITL 3 FAMILY JRNL REF ACTA CRYSTALLOGR F STRUCT V. 73 347 2017 JRNL REF 2 BIOL COMMUN JRNL REFN ESSN 2053-230X JRNL PMID 28580923 JRNL DOI 10.1107/S2053230X17007336 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 105.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 50047 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) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2649 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3661 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3280 REMARK 3 BIN FREE R VALUE SET COUNT : 204 REMARK 3 BIN FREE R VALUE : 0.3620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5458 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 90 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.17000 REMARK 3 B22 (A**2) : 0.17000 REMARK 3 B33 (A**2) : -0.35000 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): 0.204 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.183 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.156 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.907 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5610 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5249 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7610 ; 1.656 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12190 ; 1.028 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 678 ; 7.279 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 262 ;37.676 ;23.893 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1002 ;16.007 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 45 ;16.692 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 853 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6136 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1115 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2715 ; 2.160 ; 4.826 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2714 ; 2.160 ; 4.826 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3392 ; 3.415 ; 7.230 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3393 ; 3.415 ; 7.231 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2895 ; 2.130 ; 5.110 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2888 ; 2.119 ; 5.100 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4207 ; 3.408 ; 7.559 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6217 ; 5.677 ;56.218 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6204 ; 5.669 ;56.186 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 114 A 792 REMARK 3 ORIGIN FOR THE GROUP (A): 19.8432 -21.7664 27.9568 REMARK 3 T TENSOR REMARK 3 T11: 0.0719 T22: 0.0774 REMARK 3 T33: 0.1643 T12: -0.0719 REMARK 3 T13: -0.0067 T23: 0.0247 REMARK 3 L TENSOR REMARK 3 L11: 0.3595 L22: 0.2140 REMARK 3 L33: 0.8496 L12: 0.2125 REMARK 3 L13: -0.1859 L23: -0.3574 REMARK 3 S TENSOR REMARK 3 S11: -0.1312 S12: 0.1538 S13: 0.0565 REMARK 3 S21: -0.1095 S22: 0.1116 S23: -0.0088 REMARK 3 S31: 0.1796 S32: -0.1602 S33: 0.0196 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5XDR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1300003334. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-16 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31906 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 105.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, LITHIUM SULFATE, SODIUM REMARK 280 ACETATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 105.53900 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 105.53900 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 40.95950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.68850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.95950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.68850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 105.53900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.95950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.68850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 105.53900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.95950 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.68850 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: 170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 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 GLY A 106 REMARK 465 PRO A 107 REMARK 465 GLU A 108 REMARK 465 PHE A 109 REMARK 465 SER A 110 REMARK 465 LEU A 111 REMARK 465 PRO A 112 REMARK 465 GLN A 113 REMARK 465 SER A 793 REMARK 465 GLN A 794 REMARK 465 TYR A 795 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 126 NH1 NH2 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 989 O HOH A 989 3555 1.65 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 222 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 222 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 669 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 675 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 690 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 690 NE - CZ - NH2 ANGL. DEV. = -3.9 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 PRO A 184 88.27 -58.39 REMARK 500 GLN A 215 -100.35 -98.57 REMARK 500 PHE A 223 -7.69 69.08 REMARK 500 ASP A 248 75.36 -158.79 REMARK 500 ARG A 265 42.68 37.47 REMARK 500 ASP A 296 -161.09 -76.83 REMARK 500 PHE A 300 -66.88 56.46 REMARK 500 PRO A 318 142.62 -39.10 REMARK 500 ARG A 329 -66.03 -102.15 REMARK 500 MET A 344 -54.53 -137.27 REMARK 500 ASP A 375 91.88 -67.05 REMARK 500 LEU A 376 137.00 134.18 REMARK 500 GLN A 395 -16.42 -45.39 REMARK 500 ASN A 410 -62.99 -98.54 REMARK 500 ASN A 422 14.38 -59.46 REMARK 500 LYS A 443 91.13 -68.55 REMARK 500 THR A 476 -58.83 -143.38 REMARK 500 PHE A 482 75.21 -100.35 REMARK 500 LEU A 484 54.37 -96.98 REMARK 500 TYR A 490 -64.84 177.46 REMARK 500 CYS A 583 29.88 -150.28 REMARK 500 GLN A 598 124.60 -25.95 REMARK 500 ALA A 606 56.20 -143.04 REMARK 500 GLN A 700 71.01 -106.13 REMARK 500 THR A 742 -132.32 -120.78 REMARK 500 THR A 749 86.87 67.24 REMARK 500 CYS A 774 175.93 175.30 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 ASP A 374 ASP A 375 138.00 REMARK 500 REMARK 500 REMARK: NULL 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 804 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 167 OG1 REMARK 620 2 ADP A 801 O3B 83.6 REMARK 620 3 HOH A 904 O 85.9 73.5 REMARK 620 4 HOH A 922 O 167.6 86.8 83.8 REMARK 620 5 HOH A 926 O 106.4 111.7 166.9 84.6 REMARK 620 6 HOH A 936 O 94.6 147.0 73.5 89.1 100.5 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 ADP A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 804 DBREF 5XDR A 110 795 UNP O43143 DHX15_HUMAN 110 795 SEQADV 5XDR GLY A 106 UNP O43143 EXPRESSION TAG SEQADV 5XDR PRO A 107 UNP O43143 EXPRESSION TAG SEQADV 5XDR GLU A 108 UNP O43143 EXPRESSION TAG SEQADV 5XDR PHE A 109 UNP O43143 EXPRESSION TAG SEQADV 5XDR SER A 678 UNP O43143 THR 678 ENGINEERED MUTATION SEQRES 1 A 690 GLY PRO GLU PHE SER LEU PRO GLN CYS ILE ASN PRO PHE SEQRES 2 A 690 THR ASN LEU PRO HIS THR PRO ARG TYR TYR ASP ILE LEU SEQRES 3 A 690 LYS LYS ARG LEU GLN LEU PRO VAL TRP GLU TYR LYS ASP SEQRES 4 A 690 ARG PHE THR ASP ILE LEU VAL ARG HIS GLN SER PHE VAL SEQRES 5 A 690 LEU VAL GLY GLU THR GLY SER GLY LYS THR THR GLN ILE SEQRES 6 A 690 PRO GLN TRP CYS VAL GLU TYR MET ARG SER LEU PRO GLY SEQRES 7 A 690 PRO LYS ARG GLY VAL ALA CYS THR GLN PRO ARG ARG VAL SEQRES 8 A 690 ALA ALA MET SER VAL ALA GLN ARG VAL ALA ASP GLU MET SEQRES 9 A 690 ASP VAL MET LEU GLY GLN GLU VAL GLY TYR SER ILE ARG SEQRES 10 A 690 PHE GLU ASP CYS SER SER ALA LYS THR ILE LEU LYS TYR SEQRES 11 A 690 MET THR ASP GLY MET LEU LEU ARG GLU ALA MET ASN ASP SEQRES 12 A 690 PRO LEU LEU GLU ARG TYR GLY VAL ILE ILE LEU ASP GLU SEQRES 13 A 690 ALA HIS GLU ARG THR LEU ALA THR ASP ILE LEU MET GLY SEQRES 14 A 690 VAL LEU LYS GLU VAL VAL ARG GLN ARG SER ASP LEU LYS SEQRES 15 A 690 VAL ILE VAL MET SER ALA THR LEU ASP ALA GLY LYS PHE SEQRES 16 A 690 GLN ILE TYR PHE ASP ASN CYS PRO LEU LEU THR ILE PRO SEQRES 17 A 690 GLY ARG THR HIS PRO VAL GLU ILE PHE TYR THR PRO GLU SEQRES 18 A 690 PRO GLU ARG ASP TYR LEU GLU ALA ALA ILE ARG THR VAL SEQRES 19 A 690 ILE GLN ILE HIS MET CYS GLU GLU GLU GLU GLY ASP LEU SEQRES 20 A 690 LEU LEU PHE LEU THR GLY GLN GLU GLU ILE ASP GLU ALA SEQRES 21 A 690 CYS LYS ARG ILE LYS ARG GLU VAL ASP ASP LEU GLY PRO SEQRES 22 A 690 GLU VAL GLY ASP ILE LYS ILE ILE PRO LEU TYR SER THR SEQRES 23 A 690 LEU PRO PRO GLN GLN GLN GLN ARG ILE PHE GLU PRO PRO SEQRES 24 A 690 PRO PRO LYS LYS GLN ASN GLY ALA ILE GLY ARG LYS VAL SEQRES 25 A 690 VAL VAL SER THR ASN ILE ALA GLU THR SER LEU THR ILE SEQRES 26 A 690 ASP GLY VAL VAL PHE VAL ILE ASP PRO GLY PHE ALA LYS SEQRES 27 A 690 GLN LYS VAL TYR ASN PRO ARG ILE ARG VAL GLU SER LEU SEQRES 28 A 690 LEU VAL THR ALA ILE SER LYS ALA SER ALA GLN GLN ARG SEQRES 29 A 690 ALA GLY ARG ALA GLY ARG THR ARG PRO GLY LYS CYS PHE SEQRES 30 A 690 ARG LEU TYR THR GLU LYS ALA TYR LYS THR GLU MET GLN SEQRES 31 A 690 ASP ASN THR TYR PRO GLU ILE LEU ARG SER ASN LEU GLY SEQRES 32 A 690 SER VAL VAL LEU GLN LEU LYS LYS LEU GLY ILE ASP ASP SEQRES 33 A 690 LEU VAL HIS PHE ASP PHE MET ASP PRO PRO ALA PRO GLU SEQRES 34 A 690 THR LEU MET ARG ALA LEU GLU LEU LEU ASN TYR LEU ALA SEQRES 35 A 690 ALA LEU ASN ASP ASP GLY ASP LEU THR GLU LEU GLY SER SEQRES 36 A 690 MET MET ALA GLU PHE PRO LEU ASP PRO GLN LEU ALA LYS SEQRES 37 A 690 MET VAL ILE ALA SER CYS ASP TYR ASN CYS SER ASN GLU SEQRES 38 A 690 VAL LEU SER ILE THR ALA MET LEU SER VAL PRO GLN CYS SEQRES 39 A 690 PHE VAL ARG PRO THR GLU ALA LYS LYS ALA ALA ASP GLU SEQRES 40 A 690 ALA LYS MET ARG PHE ALA HIS ILE ASP GLY ASP HIS LEU SEQRES 41 A 690 THR LEU LEU ASN VAL TYR HIS ALA PHE LYS GLN ASN HIS SEQRES 42 A 690 GLU SER VAL GLN TRP CYS TYR ASP ASN PHE ILE ASN TYR SEQRES 43 A 690 ARG SER LEU MET SER ALA ASP ASN VAL ARG GLN GLN LEU SEQRES 44 A 690 SER ARG ILE MET ASP ARG PHE ASN LEU PRO ARG ARG SER SEQRES 45 A 690 SER ASP PHE THR SER ARG ASP TYR TYR ILE ASN ILE ARG SEQRES 46 A 690 LYS ALA LEU VAL THR GLY TYR PHE MET GLN VAL ALA HIS SEQRES 47 A 690 LEU GLU ARG THR GLY HIS TYR LEU THR VAL LYS ASP ASN SEQRES 48 A 690 GLN VAL VAL GLN LEU HIS PRO SER THR VAL LEU ASP HIS SEQRES 49 A 690 LYS PRO GLU TRP VAL LEU TYR ASN GLU PHE VAL LEU THR SEQRES 50 A 690 THR LYS ASN TYR ILE ARG THR CYS THR ASP ILE LYS PRO SEQRES 51 A 690 GLU TRP LEU VAL LYS ILE ALA PRO GLN TYR TYR ASP MET SEQRES 52 A 690 SER ASN PHE PRO GLN CYS GLU ALA LYS ARG GLN LEU ASP SEQRES 53 A 690 ARG ILE ILE ALA LYS LEU GLN SER LYS GLU TYR SER GLN SEQRES 54 A 690 TYR HET ADP A 801 27 HET SO4 A 802 5 HET SO4 A 803 5 HET MG A 804 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 MG MG 2+ FORMUL 6 HOH *90(H2 O) HELIX 1 AA1 THR A 124 LEU A 135 1 12 HELIX 2 AA2 GLN A 136 GLU A 141 5 6 HELIX 3 AA3 TYR A 142 VAL A 151 1 10 HELIX 4 AA4 GLY A 165 SER A 180 1 16 HELIX 5 AA5 ARG A 194 MET A 209 1 16 HELIX 6 AA6 ASP A 238 ASN A 247 1 10 HELIX 7 AA7 GLU A 261 ARG A 265 5 5 HELIX 8 AA8 THR A 266 ARG A 283 1 18 HELIX 9 AA9 ASP A 330 GLU A 346 1 17 HELIX 10 AB1 GLU A 360 ARG A 368 1 9 HELIX 11 AB2 PRO A 393 GLN A 398 1 6 HELIX 12 AB3 ASN A 422 SER A 427 1 6 HELIX 13 AB4 SER A 462 ARG A 472 1 11 HELIX 14 AB5 ALA A 473 ARG A 475 5 3 HELIX 15 AB6 PRO A 500 ARG A 504 5 5 HELIX 16 AB7 LEU A 507 LEU A 517 1 11 HELIX 17 AB8 ALA A 532 LEU A 546 1 15 HELIX 18 AB9 THR A 556 ALA A 563 1 8 HELIX 19 AC1 ASP A 568 CYS A 579 1 12 HELIX 20 AC2 ASP A 580 ASN A 582 5 3 HELIX 21 AC3 CYS A 583 SER A 595 1 13 HELIX 22 AC4 PRO A 603 GLU A 605 5 3 HELIX 23 AC5 ALA A 606 ARG A 616 1 11 HELIX 24 AC6 GLY A 622 ASN A 637 1 16 HELIX 25 AC7 SER A 640 ASN A 647 1 8 HELIX 26 AC8 ASN A 650 PHE A 671 1 22 HELIX 27 AC9 ARG A 683 PHE A 698 1 16 HELIX 28 AD1 LYS A 754 ALA A 762 1 9 HELIX 29 AD2 ASP A 767 PHE A 771 5 5 HELIX 30 AD3 CYS A 774 SER A 789 1 16 SHEET 1 AA1 2 ILE A 115 ASN A 116 0 SHEET 2 AA1 2 LEU A 121 PRO A 122 -1 O LEU A 121 N ASN A 116 SHEET 1 AA2 8 GLU A 224 CYS A 226 0 SHEET 2 AA2 8 VAL A 217 ILE A 221 -1 N ILE A 221 O GLU A 224 SHEET 3 AA2 8 LEU A 233 THR A 237 1 O TYR A 235 N GLY A 218 SHEET 4 AA2 8 GLY A 187 GLN A 192 1 N VAL A 188 O LYS A 234 SHEET 5 AA2 8 TYR A 254 LEU A 259 1 O ILE A 258 N ALA A 189 SHEET 6 AA2 8 LYS A 287 SER A 292 1 O LYS A 287 N ILE A 257 SHEET 7 AA2 8 SER A 155 GLY A 160 1 N LEU A 158 O VAL A 290 SHEET 8 AA2 8 LEU A 309 ILE A 312 1 O LEU A 310 N VAL A 159 SHEET 1 AA3 6 VAL A 319 PHE A 322 0 SHEET 2 AA3 6 GLY A 479 ARG A 483 1 O GLY A 479 N GLU A 320 SHEET 3 AA3 6 VAL A 433 ASP A 438 1 N VAL A 436 O PHE A 482 SHEET 4 AA3 6 ASP A 351 PHE A 355 1 N LEU A 353 O PHE A 435 SHEET 5 AA3 6 ARG A 415 SER A 420 1 O VAL A 418 N LEU A 352 SHEET 6 AA3 6 ILE A 383 LEU A 388 1 N ILE A 386 O VAL A 419 SHEET 1 AA4 2 PHE A 441 ASN A 448 0 SHEET 2 AA4 2 VAL A 453 ALA A 460 -1 O LEU A 457 N GLN A 444 SHEET 1 AA5 6 VAL A 701 LEU A 704 0 SHEET 2 AA5 6 TYR A 710 THR A 712 -1 O LEU A 711 N HIS A 703 SHEET 3 AA5 6 VAL A 718 LEU A 721 -1 O VAL A 719 N TYR A 710 SHEET 4 AA5 6 ASN A 745 ASP A 752 1 O ASN A 745 N GLN A 720 SHEET 5 AA5 6 TRP A 733 LEU A 741 -1 N VAL A 740 O TYR A 746 SHEET 6 AA5 6 VAL A 701 LEU A 704 -1 N ALA A 702 O VAL A 734 LINK OG1 THR A 167 MG MG A 804 1555 1555 1.97 LINK O3B ADP A 801 MG MG A 804 1555 1555 2.27 LINK MG MG A 804 O HOH A 904 1555 1555 1.94 LINK MG MG A 804 O HOH A 922 1555 1555 2.13 LINK MG MG A 804 O HOH A 926 1555 1555 1.91 LINK MG MG A 804 O HOH A 936 1555 1555 2.42 CISPEP 1 GLU A 372 VAL A 373 0 2.62 SITE 1 AC1 15 THR A 162 GLY A 163 SER A 164 GLY A 165 SITE 2 AC1 15 LYS A 166 THR A 167 THR A 168 SER A 200 SITE 3 AC1 15 ARG A 204 PHE A 401 ASP A 431 ARG A 475 SITE 4 AC1 15 MG A 804 HOH A 904 HOH A 922 SITE 1 AC2 2 ARG A 602 LYS A 607 SITE 1 AC3 4 LYS A 691 LYS A 754 TRP A 757 HOH A 944 SITE 1 AC4 7 THR A 167 ASP A 260 ADP A 801 HOH A 904 SITE 2 AC4 7 HOH A 922 HOH A 926 HOH A 936 CRYST1 81.919 89.377 211.078 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 0.012207 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011189 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004738 0.00000