PDB Short entry for 3VYX HEADER HYDROLASE/RNA 05-OCT-12 3VYX TITLE STRUCTURAL INSIGHTS INTO RISC ASSEMBLY FACILITATED BY DSRNA BINDING TITLE 2 DOMAINS OF HUMAN RNA HELICASE (DHX9) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT RNA HELICASE A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 152-264; COMPND 5 SYNONYM: RHA, DEAH BOX PROTEIN 9, LEUKOPHYSIN, LKP, NUCLEAR DNA COMPND 6 HELICASE II, NDH II; COMPND 7 EC: 3.6.4.13; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: RNA (5'-R(P*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3'); COMPND 11 CHAIN: B, C; COMPND 12 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: DHX9, DDX9, LKP, NDH2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 OTHER_DETAILS: THIS SEQUENCE IS SYNTHESIZED IN VITRO. KEYWDS PROTEIN-DSRNA COMPLEX, DSRBD FOLD, DSRNA BINDING, PROTEIN-PROTEIN KEYWDS 2 INTERACTION, HYDROLASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.A.YUAN,Q.FU REVDAT 4 20-MAR-24 3VYX 1 COMPND SOURCE REVDAT 3 08-NOV-23 3VYX 1 REMARK REVDAT 2 24-AUG-22 3VYX 1 JRNL SEQADV REVDAT 1 13-FEB-13 3VYX 0 JRNL AUTH Q.FU,Y.A.YUAN JRNL TITL STRUCTURAL INSIGHTS INTO RISC ASSEMBLY FACILITATED BY JRNL TITL 2 DSRNA-BINDING DOMAINS OF HUMAN RNA HELICASE A (DHX9). JRNL REF NUCLEIC ACIDS RES. V. 41 3457 2013 JRNL REFN ESSN 1362-4962 JRNL PMID 23361462 JRNL DOI 10.1093/NAR/GKT042 REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 9800 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 497 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) : 2.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.35 REMARK 3 REFLECTION IN BIN (WORKING SET) : 696 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.06 REMARK 3 BIN R VALUE (WORKING SET) : 0.2180 REMARK 3 BIN FREE R VALUE SET COUNT : 38 REMARK 3 BIN FREE R VALUE : 0.3620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 765 REMARK 3 NUCLEIC ACID ATOMS : 432 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 82 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.29000 REMARK 3 B22 (A**2) : 1.29000 REMARK 3 B33 (A**2) : -2.57000 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): 0.235 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.222 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.143 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.204 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1260 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1796 ; 1.715 ; 2.377 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 94 ; 6.694 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 40 ;34.245 ;23.500 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 140 ;17.337 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;25.845 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 210 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 803 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 485 ; 0.191 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 835 ; 0.286 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 70 ; 0.193 ; 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): 45 ; 0.133 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.213 ; 0.200 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): 480 ; 0.959 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 740 ; 1.524 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1042 ; 1.932 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1056 ; 2.698 ; 4.500 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 : A 169 A 263 REMARK 3 ORIGIN FOR THE GROUP (A): 8.1503 -14.1253 -12.1455 REMARK 3 T TENSOR REMARK 3 T11: 0.0259 T22: -0.1244 REMARK 3 T33: -0.0333 T12: 0.0467 REMARK 3 T13: 0.0216 T23: 0.0159 REMARK 3 L TENSOR REMARK 3 L11: 0.9803 L22: 1.4360 REMARK 3 L33: 6.3012 L12: 0.3237 REMARK 3 L13: 0.9891 L23: -0.9249 REMARK 3 S TENSOR REMARK 3 S11: -0.0684 S12: 0.0618 S13: 0.0172 REMARK 3 S21: 0.3851 S22: 0.1406 S23: 0.1412 REMARK 3 S31: -0.3765 S32: -0.1047 S33: -0.0722 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 10 REMARK 3 ORIGIN FOR THE GROUP (A): -1.1128 -30.3301 -5.1455 REMARK 3 T TENSOR REMARK 3 T11: 0.0147 T22: 0.0582 REMARK 3 T33: -0.0226 T12: -0.0337 REMARK 3 T13: 0.0167 T23: 0.1159 REMARK 3 L TENSOR REMARK 3 L11: 0.0044 L22: 0.5870 REMARK 3 L33: 2.1991 L12: -0.0029 REMARK 3 L13: 0.0980 L23: -0.1225 REMARK 3 S TENSOR REMARK 3 S11: 0.2396 S12: 0.1381 S13: 0.1469 REMARK 3 S21: -0.1233 S22: 0.2096 S23: 0.0458 REMARK 3 S31: 0.4140 S32: -0.5608 S33: -0.4492 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 : C 1 C 10 REMARK 3 ORIGIN FOR THE GROUP (A): 0.1087 -30.8968 -2.0893 REMARK 3 T TENSOR REMARK 3 T11: -0.0004 T22: -0.0004 REMARK 3 T33: -0.0435 T12: 0.0654 REMARK 3 T13: 0.0748 T23: 0.0920 REMARK 3 L TENSOR REMARK 3 L11: 1.6699 L22: 1.9038 REMARK 3 L33: 1.9420 L12: -0.7089 REMARK 3 L13: -0.0056 L23: -0.9935 REMARK 3 S TENSOR REMARK 3 S11: 0.1330 S12: -0.1063 S13: 0.1020 REMARK 3 S21: 0.4210 S22: 0.2214 S23: 0.1125 REMARK 3 S31: 0.1896 S32: -0.2084 S33: -0.3544 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 3VYX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000095674. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9800 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.290 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.32200 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: 1UIL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, KNO3, TRIS, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 53.80850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.59900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.59900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 80.71275 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.59900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.59900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.90425 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.59900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.59900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 80.71275 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.59900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.59900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.90425 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 53.80850 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 MET A 151 REMARK 465 LYS A 152 REMARK 465 GLU A 153 REMARK 465 GLU A 154 REMARK 465 GLN A 155 REMARK 465 GLU A 156 REMARK 465 VAL A 157 REMARK 465 GLN A 158 REMARK 465 ALA A 159 REMARK 465 THR A 160 REMARK 465 LEU A 161 REMARK 465 GLU A 162 REMARK 465 SER A 163 REMARK 465 GLU A 164 REMARK 465 GLU A 165 REMARK 465 VAL A 166 REMARK 465 ASP A 167 REMARK 465 LEU A 168 REMARK 465 LYS A 264 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 GLY A 204 NH1 ARG A 209 1.87 REMARK 500 OD1 ASP A 206 NH2 ARG A 209 1.97 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 G B 1 P G B 1 OP3 -0.124 REMARK 500 G C 1 P G C 1 OP3 -0.131 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 G B 5 C4' - C3' - C2' ANGL. DEV. = -6.9 DEGREES REMARK 500 G C 1 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 C C 8 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 C C 10 O4' - C1' - N1 ANGL. DEV. = 5.5 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 ASN A 208 53.35 -146.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VYY RELATED DB: PDB DBREF 3VYX A 152 264 UNP Q08211 DHX9_HUMAN 152 264 DBREF 3VYX B 1 10 PDB 3VYX 3VYX 1 10 DBREF 3VYX C 1 10 PDB 3VYX 3VYX 1 10 SEQADV 3VYX MET A 151 UNP Q08211 EXPRESSION TAG SEQRES 1 A 114 MET LYS GLU GLU GLN GLU VAL GLN ALA THR LEU GLU SER SEQRES 2 A 114 GLU GLU VAL ASP LEU ASN ALA GLY LEU HIS GLY ASN TRP SEQRES 3 A 114 THR LEU GLU ASN ALA LYS ALA ARG LEU ASN GLN TYR PHE SEQRES 4 A 114 GLN LYS GLU LYS ILE GLN GLY GLU TYR LYS TYR THR GLN SEQRES 5 A 114 VAL GLY PRO ASP HIS ASN ARG SER PHE ILE ALA GLU MET SEQRES 6 A 114 THR ILE TYR ILE LYS GLN LEU GLY ARG ARG ILE PHE ALA SEQRES 7 A 114 ARG GLU HIS GLY SER ASN LYS LYS LEU ALA ALA GLN SER SEQRES 8 A 114 CYS ALA LEU SER LEU VAL ARG GLN LEU TYR HIS LEU GLY SEQRES 9 A 114 VAL VAL GLU ALA TYR SER GLY LEU THR LYS SEQRES 1 B 10 G C G C G C G C G C SEQRES 1 C 10 G C G C G C G C G C FORMUL 4 HOH *82(H2 O) HELIX 1 1 ASN A 169 GLY A 174 5 6 HELIX 2 2 ASN A 180 GLU A 192 1 13 HELIX 3 3 PRO A 205 ARG A 209 5 5 HELIX 4 4 LYS A 220 GLY A 223 5 4 HELIX 5 5 ASN A 234 LEU A 253 1 20 SHEET 1 A 3 LYS A 199 VAL A 203 0 SHEET 2 A 3 SER A 210 TYR A 218 -1 O ILE A 212 N THR A 201 SHEET 3 A 3 ARG A 225 GLY A 232 -1 O ILE A 226 N ILE A 217 CRYST1 63.198 63.198 107.617 90.00 90.00 90.00 P 43 21 2 16 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 0.015823 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015823 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009292 0.00000