HEADER HYDROLASE 06-SEP-16 5GVS TITLE CRYSTAL STRUCTURE OF THE DDX41 DEAD DOMAIN IN AN APO OPEN FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE ATP-DEPENDENT RNA HELICASE DDX41; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: UNP RESIDUES 169-399; COMPND 5 SYNONYM: DEAD BOX PROTEIN 41,DEAD BOX PROTEIN ABSTRAKT HOMOLOG; COMPND 6 EC: 3.6.4.13; 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: DDX41, ABS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS ATPASE, DEAD BOX PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.OMURA,D.OIKAWA,T.NAKANE,M.KATO,R.ISHII,Y.GOTO,H.SUGA,R.ISHITANI, AUTHOR 2 F.TOKUNAGA,O.NUREKI REVDAT 3 08-NOV-23 5GVS 1 REMARK REVDAT 2 26-FEB-20 5GVS 1 REMARK REVDAT 1 19-OCT-16 5GVS 0 JRNL AUTH H.OMURA,D.OIKAWA,T.NAKANE,M.KATO,R.ISHII,R.ISHITANI, JRNL AUTH 2 F.TOKUNAGA,O.NUREKI JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF DDX41: A BISPECIFIC JRNL TITL 2 IMMUNE RECEPTOR FOR DNA AND CYCLIC DINUCLEOTIDE JRNL REF SCI REP V. 6 34756 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27721487 JRNL DOI 10.1038/SREP34756 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0151 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 76.1 REMARK 3 NUMBER OF REFLECTIONS : 34370 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1824 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2536 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE SET COUNT : 120 REMARK 3 BIN FREE R VALUE : 0.2890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6473 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 233 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.70000 REMARK 3 B22 (A**2) : -1.42000 REMARK 3 B33 (A**2) : -0.21000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.38000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.479 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.298 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.204 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.371 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.882 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6583 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6708 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8828 ; 1.696 ; 1.997 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15462 ; 1.020 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 820 ; 6.997 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 248 ;31.440 ;22.500 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1298 ;15.989 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 56 ;17.157 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1009 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7128 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1424 ; 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): 3298 ; 1.944 ; 2.285 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3297 ; 1.943 ; 2.285 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4112 ; 3.396 ; 3.419 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4113 ; 3.396 ; 3.419 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3285 ; 1.991 ; 2.581 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3286 ; 1.991 ; 2.581 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4716 ; 3.375 ; 3.738 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7142 ; 6.053 ;27.111 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7096 ; 6.042 ;27.087 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 : 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 5GVS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1300001449. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-APR-14 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 : SPRING-8 REMARK 200 BEAMLINE : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36258 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 49.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 76.5 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.20200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5GVR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRI-AMMONIUM CITRATE, PEG 3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 35.86727 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.48000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 100.83144 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.86727 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.48000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 100.83144 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 ILE A 169 REMARK 465 LEU A 170 REMARK 465 VAL A 171 REMARK 465 GLU A 172 REMARK 465 GLY A 173 REMARK 465 ASP A 174 REMARK 465 GLY A 175 REMARK 465 ILE A 176 REMARK 465 PRO A 177 REMARK 465 PRO A 178 REMARK 465 PRO A 179 REMARK 465 ILE A 180 REMARK 465 LYS A 181 REMARK 465 SER A 182 REMARK 465 PHE A 183 REMARK 465 ILE B 169 REMARK 465 LEU B 170 REMARK 465 VAL B 171 REMARK 465 GLU B 172 REMARK 465 GLY B 173 REMARK 465 ASP B 174 REMARK 465 GLY B 175 REMARK 465 ILE B 176 REMARK 465 PRO B 177 REMARK 465 PRO B 178 REMARK 465 PRO B 179 REMARK 465 ILE B 180 REMARK 465 LYS B 181 REMARK 465 SER B 182 REMARK 465 PHE B 183 REMARK 465 LYS B 184 REMARK 465 ILE C 169 REMARK 465 LEU C 170 REMARK 465 VAL C 171 REMARK 465 GLU C 172 REMARK 465 GLY C 173 REMARK 465 ASP C 174 REMARK 465 GLY C 175 REMARK 465 ILE C 176 REMARK 465 PRO C 177 REMARK 465 PRO C 178 REMARK 465 PRO C 179 REMARK 465 ILE C 180 REMARK 465 LYS C 181 REMARK 465 SER C 182 REMARK 465 PHE C 183 REMARK 465 LYS C 184 REMARK 465 GLU C 185 REMARK 465 MET C 186 REMARK 465 LYS C 187 REMARK 465 PHE C 188 REMARK 465 PRO C 189 REMARK 465 ALA C 190 REMARK 465 GLY C 200 REMARK 465 ILE C 201 REMARK 465 HIS C 202 REMARK 465 HIS C 203 REMARK 465 PRO C 204 REMARK 465 THR C 205 REMARK 465 PRO C 206 REMARK 465 ILE C 207 REMARK 465 GLN C 208 REMARK 465 ILE C 209 REMARK 465 GLN C 210 REMARK 465 ILE D 169 REMARK 465 LEU D 170 REMARK 465 VAL D 171 REMARK 465 GLU D 172 REMARK 465 GLY D 173 REMARK 465 ASP D 174 REMARK 465 GLY D 175 REMARK 465 ILE D 176 REMARK 465 PRO D 177 REMARK 465 PRO D 178 REMARK 465 PRO D 179 REMARK 465 ILE D 180 REMARK 465 LYS D 181 REMARK 465 SER D 182 REMARK 465 PHE D 183 REMARK 465 LYS D 184 REMARK 465 GLU D 185 REMARK 465 MET D 186 REMARK 465 LYS D 187 REMARK 465 PHE D 188 REMARK 465 PRO D 189 REMARK 465 ALA D 190 REMARK 465 GLY D 200 REMARK 465 ILE D 201 REMARK 465 HIS D 202 REMARK 465 HIS D 203 REMARK 465 PRO D 204 REMARK 465 THR D 205 REMARK 465 PRO D 206 REMARK 465 ILE D 207 REMARK 465 GLN D 208 REMARK 465 ILE D 209 REMARK 465 GLN D 210 REMARK 465 GLY D 211 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS D 199 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O LYS D 304 OE1 GLU D 308 1.87 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 B 249 NE - CZ - NH2 ANGL. DEV. = 3.1 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 ASP A 287 55.65 -95.74 REMARK 500 ASP B 287 53.52 -105.57 REMARK 500 HIS B 312 36.45 -90.20 REMARK 500 PRO C 213 43.19 -80.20 REMARK 500 THR C 309 -72.76 -133.84 REMARK 500 ILE C 310 53.41 -107.40 REMARK 500 LYS D 197 119.69 -30.38 REMARK 500 PRO D 213 40.55 -85.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GVR RELATED DB: PDB DBREF 5GVS A 169 399 UNP Q9UJV9 DDX41_HUMAN 169 399 DBREF 5GVS B 169 399 UNP Q9UJV9 DDX41_HUMAN 169 399 DBREF 5GVS C 169 399 UNP Q9UJV9 DDX41_HUMAN 169 399 DBREF 5GVS D 169 399 UNP Q9UJV9 DDX41_HUMAN 169 399 SEQRES 1 A 231 ILE LEU VAL GLU GLY ASP GLY ILE PRO PRO PRO ILE LYS SEQRES 2 A 231 SER PHE LYS GLU MET LYS PHE PRO ALA ALA ILE LEU ARG SEQRES 3 A 231 GLY LEU LYS LYS LYS GLY ILE HIS HIS PRO THR PRO ILE SEQRES 4 A 231 GLN ILE GLN GLY ILE PRO THR ILE LEU SER GLY ARG ASP SEQRES 5 A 231 MET ILE GLY ILE ALA PHE THR GLY SER GLY LYS THR LEU SEQRES 6 A 231 VAL PHE THR LEU PRO VAL ILE MET PHE CYS LEU GLU GLN SEQRES 7 A 231 GLU LYS ARG LEU PRO PHE SER LYS ARG GLU GLY PRO TYR SEQRES 8 A 231 GLY LEU ILE ILE CYS PRO SER ARG GLU LEU ALA ARG GLN SEQRES 9 A 231 THR HIS GLY ILE LEU GLU TYR TYR CYS ARG LEU LEU GLN SEQRES 10 A 231 GLU ASP SER SER PRO LEU LEU ARG CYS ALA LEU CYS ILE SEQRES 11 A 231 GLY GLY MET SER VAL LYS GLU GLN MET GLU THR ILE ARG SEQRES 12 A 231 HIS GLY VAL HIS MET MET VAL ALA THR PRO GLY ARG LEU SEQRES 13 A 231 MET ASP LEU LEU GLN LYS LYS MET VAL SER LEU ASP ILE SEQRES 14 A 231 CYS ARG TYR LEU ALA LEU ASP GLU ALA ASP ARG MET ILE SEQRES 15 A 231 ASP MET GLY PHE GLU GLY ASP ILE ARG THR ILE PHE SER SEQRES 16 A 231 TYR PHE LYS GLY GLN ARG GLN THR LEU LEU PHE SER ALA SEQRES 17 A 231 THR MET PRO LYS LYS ILE GLN ASN PHE ALA LYS SER ALA SEQRES 18 A 231 LEU VAL LYS PRO VAL THR ILE ASN VAL GLY SEQRES 1 B 231 ILE LEU VAL GLU GLY ASP GLY ILE PRO PRO PRO ILE LYS SEQRES 2 B 231 SER PHE LYS GLU MET LYS PHE PRO ALA ALA ILE LEU ARG SEQRES 3 B 231 GLY LEU LYS LYS LYS GLY ILE HIS HIS PRO THR PRO ILE SEQRES 4 B 231 GLN ILE GLN GLY ILE PRO THR ILE LEU SER GLY ARG ASP SEQRES 5 B 231 MET ILE GLY ILE ALA PHE THR GLY SER GLY LYS THR LEU SEQRES 6 B 231 VAL PHE THR LEU PRO VAL ILE MET PHE CYS LEU GLU GLN SEQRES 7 B 231 GLU LYS ARG LEU PRO PHE SER LYS ARG GLU GLY PRO TYR SEQRES 8 B 231 GLY LEU ILE ILE CYS PRO SER ARG GLU LEU ALA ARG GLN SEQRES 9 B 231 THR HIS GLY ILE LEU GLU TYR TYR CYS ARG LEU LEU GLN SEQRES 10 B 231 GLU ASP SER SER PRO LEU LEU ARG CYS ALA LEU CYS ILE SEQRES 11 B 231 GLY GLY MET SER VAL LYS GLU GLN MET GLU THR ILE ARG SEQRES 12 B 231 HIS GLY VAL HIS MET MET VAL ALA THR PRO GLY ARG LEU SEQRES 13 B 231 MET ASP LEU LEU GLN LYS LYS MET VAL SER LEU ASP ILE SEQRES 14 B 231 CYS ARG TYR LEU ALA LEU ASP GLU ALA ASP ARG MET ILE SEQRES 15 B 231 ASP MET GLY PHE GLU GLY ASP ILE ARG THR ILE PHE SER SEQRES 16 B 231 TYR PHE LYS GLY GLN ARG GLN THR LEU LEU PHE SER ALA SEQRES 17 B 231 THR MET PRO LYS LYS ILE GLN ASN PHE ALA LYS SER ALA SEQRES 18 B 231 LEU VAL LYS PRO VAL THR ILE ASN VAL GLY SEQRES 1 C 231 ILE LEU VAL GLU GLY ASP GLY ILE PRO PRO PRO ILE LYS SEQRES 2 C 231 SER PHE LYS GLU MET LYS PHE PRO ALA ALA ILE LEU ARG SEQRES 3 C 231 GLY LEU LYS LYS LYS GLY ILE HIS HIS PRO THR PRO ILE SEQRES 4 C 231 GLN ILE GLN GLY ILE PRO THR ILE LEU SER GLY ARG ASP SEQRES 5 C 231 MET ILE GLY ILE ALA PHE THR GLY SER GLY LYS THR LEU SEQRES 6 C 231 VAL PHE THR LEU PRO VAL ILE MET PHE CYS LEU GLU GLN SEQRES 7 C 231 GLU LYS ARG LEU PRO PHE SER LYS ARG GLU GLY PRO TYR SEQRES 8 C 231 GLY LEU ILE ILE CYS PRO SER ARG GLU LEU ALA ARG GLN SEQRES 9 C 231 THR HIS GLY ILE LEU GLU TYR TYR CYS ARG LEU LEU GLN SEQRES 10 C 231 GLU ASP SER SER PRO LEU LEU ARG CYS ALA LEU CYS ILE SEQRES 11 C 231 GLY GLY MET SER VAL LYS GLU GLN MET GLU THR ILE ARG SEQRES 12 C 231 HIS GLY VAL HIS MET MET VAL ALA THR PRO GLY ARG LEU SEQRES 13 C 231 MET ASP LEU LEU GLN LYS LYS MET VAL SER LEU ASP ILE SEQRES 14 C 231 CYS ARG TYR LEU ALA LEU ASP GLU ALA ASP ARG MET ILE SEQRES 15 C 231 ASP MET GLY PHE GLU GLY ASP ILE ARG THR ILE PHE SER SEQRES 16 C 231 TYR PHE LYS GLY GLN ARG GLN THR LEU LEU PHE SER ALA SEQRES 17 C 231 THR MET PRO LYS LYS ILE GLN ASN PHE ALA LYS SER ALA SEQRES 18 C 231 LEU VAL LYS PRO VAL THR ILE ASN VAL GLY SEQRES 1 D 231 ILE LEU VAL GLU GLY ASP GLY ILE PRO PRO PRO ILE LYS SEQRES 2 D 231 SER PHE LYS GLU MET LYS PHE PRO ALA ALA ILE LEU ARG SEQRES 3 D 231 GLY LEU LYS LYS LYS GLY ILE HIS HIS PRO THR PRO ILE SEQRES 4 D 231 GLN ILE GLN GLY ILE PRO THR ILE LEU SER GLY ARG ASP SEQRES 5 D 231 MET ILE GLY ILE ALA PHE THR GLY SER GLY LYS THR LEU SEQRES 6 D 231 VAL PHE THR LEU PRO VAL ILE MET PHE CYS LEU GLU GLN SEQRES 7 D 231 GLU LYS ARG LEU PRO PHE SER LYS ARG GLU GLY PRO TYR SEQRES 8 D 231 GLY LEU ILE ILE CYS PRO SER ARG GLU LEU ALA ARG GLN SEQRES 9 D 231 THR HIS GLY ILE LEU GLU TYR TYR CYS ARG LEU LEU GLN SEQRES 10 D 231 GLU ASP SER SER PRO LEU LEU ARG CYS ALA LEU CYS ILE SEQRES 11 D 231 GLY GLY MET SER VAL LYS GLU GLN MET GLU THR ILE ARG SEQRES 12 D 231 HIS GLY VAL HIS MET MET VAL ALA THR PRO GLY ARG LEU SEQRES 13 D 231 MET ASP LEU LEU GLN LYS LYS MET VAL SER LEU ASP ILE SEQRES 14 D 231 CYS ARG TYR LEU ALA LEU ASP GLU ALA ASP ARG MET ILE SEQRES 15 D 231 ASP MET GLY PHE GLU GLY ASP ILE ARG THR ILE PHE SER SEQRES 16 D 231 TYR PHE LYS GLY GLN ARG GLN THR LEU LEU PHE SER ALA SEQRES 17 D 231 THR MET PRO LYS LYS ILE GLN ASN PHE ALA LYS SER ALA SEQRES 18 D 231 LEU VAL LYS PRO VAL THR ILE ASN VAL GLY FORMUL 5 HOH *233(H2 O) HELIX 1 AA1 PRO A 189 LYS A 199 1 11 HELIX 2 AA2 ILE A 215 GLY A 218 5 4 HELIX 3 AA3 THR A 227 PHE A 235 1 9 HELIX 4 AA4 PHE A 235 LYS A 248 1 14 HELIX 5 AA5 SER A 266 GLU A 286 1 21 HELIX 6 AA6 SER A 302 ARG A 311 1 10 HELIX 7 AA7 THR A 320 LYS A 330 1 11 HELIX 8 AA8 GLU A 345 MET A 352 1 8 HELIX 9 AA9 PHE A 354 SER A 363 1 10 HELIX 10 AB1 PRO A 379 LEU A 390 1 12 HELIX 11 AB2 PRO B 189 LYS B 198 1 10 HELIX 12 AB3 THR B 227 PHE B 235 1 9 HELIX 13 AB4 PHE B 235 GLU B 247 1 13 HELIX 14 AB5 LYS B 248 LEU B 250 5 3 HELIX 15 AB6 SER B 266 GLU B 286 1 21 HELIX 16 AB7 SER B 302 THR B 309 1 8 HELIX 17 AB8 THR B 320 LYS B 330 1 11 HELIX 18 AB9 GLU B 345 MET B 352 1 8 HELIX 19 AC1 PHE B 354 SER B 363 1 10 HELIX 20 AC2 PRO B 379 LEU B 390 1 12 HELIX 21 AC3 THR C 214 GLY C 218 5 5 HELIX 22 AC4 THR C 227 PHE C 235 1 9 HELIX 23 AC5 PHE C 235 LEU C 250 1 16 HELIX 24 AC6 SER C 266 GLU C 286 1 21 HELIX 25 AC7 SER C 302 GLU C 308 1 7 HELIX 26 AC8 THR C 320 LYS C 330 1 11 HELIX 27 AC9 GLU C 345 MET C 352 1 8 HELIX 28 AD1 PHE C 354 SER C 363 1 10 HELIX 29 AD2 PRO C 379 LEU C 390 1 12 HELIX 30 AD3 THR D 214 GLY D 218 5 5 HELIX 31 AD4 THR D 227 PHE D 235 1 9 HELIX 32 AD5 PHE D 235 LEU D 250 1 16 HELIX 33 AD6 SER D 266 GLU D 286 1 21 HELIX 34 AD7 SER D 302 GLU D 308 1 7 HELIX 35 AD8 THR D 320 LYS D 330 1 11 HELIX 36 AD9 GLU D 345 MET D 352 1 8 HELIX 37 AE1 PHE D 354 TYR D 364 1 11 HELIX 38 AE2 PRO D 379 LEU D 390 1 12 SHEET 1 AA1 2 GLN A 208 ILE A 209 0 SHEET 2 AA1 2 ILE A 212 PRO A 213 -1 O ILE A 212 N ILE A 209 SHEET 1 AA2 7 CYS A 294 CYS A 297 0 SHEET 2 AA2 7 MET A 316 ALA A 319 1 O VAL A 318 N CYS A 297 SHEET 3 AA2 7 GLY A 260 ILE A 263 1 N ILE A 262 O ALA A 319 SHEET 4 AA2 7 TYR A 340 LEU A 343 1 O ALA A 342 N ILE A 263 SHEET 5 AA2 7 GLN A 370 SER A 375 1 O PHE A 374 N LEU A 343 SHEET 6 AA2 7 MET A 221 ILE A 224 1 N GLY A 223 O LEU A 373 SHEET 7 AA2 7 VAL A 394 ASN A 397 1 O ILE A 396 N ILE A 222 SHEET 1 AA3 2 GLN B 208 ILE B 209 0 SHEET 2 AA3 2 ILE B 212 PRO B 213 -1 O ILE B 212 N ILE B 209 SHEET 1 AA4 7 CYS B 294 CYS B 297 0 SHEET 2 AA4 7 MET B 316 ALA B 319 1 O MET B 316 N ALA B 295 SHEET 3 AA4 7 GLY B 260 ILE B 263 1 N ILE B 262 O MET B 317 SHEET 4 AA4 7 TYR B 340 LEU B 343 1 O ALA B 342 N ILE B 263 SHEET 5 AA4 7 GLN B 370 SER B 375 1 O LEU B 372 N LEU B 341 SHEET 6 AA4 7 MET B 221 ILE B 224 1 N GLY B 223 O LEU B 373 SHEET 7 AA4 7 VAL B 394 ASN B 397 1 O ILE B 396 N ILE B 222 SHEET 1 AA5 7 CYS C 294 CYS C 297 0 SHEET 2 AA5 7 MET C 316 ALA C 319 1 O MET C 316 N ALA C 295 SHEET 3 AA5 7 GLY C 260 ILE C 263 1 N ILE C 262 O ALA C 319 SHEET 4 AA5 7 TYR C 340 LEU C 343 1 O ALA C 342 N ILE C 263 SHEET 5 AA5 7 GLN C 370 SER C 375 1 O LEU C 372 N LEU C 341 SHEET 6 AA5 7 MET C 221 ILE C 224 1 N GLY C 223 O LEU C 373 SHEET 7 AA5 7 VAL C 394 ASN C 397 1 O ILE C 396 N ILE C 224 SHEET 1 AA6 7 CYS D 294 CYS D 297 0 SHEET 2 AA6 7 MET D 316 ALA D 319 1 O MET D 316 N ALA D 295 SHEET 3 AA6 7 GLY D 260 ILE D 263 1 N ILE D 262 O ALA D 319 SHEET 4 AA6 7 TYR D 340 LEU D 343 1 O ALA D 342 N LEU D 261 SHEET 5 AA6 7 GLN D 370 SER D 375 1 O LEU D 372 N LEU D 343 SHEET 6 AA6 7 MET D 221 ILE D 224 1 N MET D 221 O LEU D 373 SHEET 7 AA6 7 VAL D 394 ASN D 397 1 O ILE D 396 N ILE D 224 CISPEP 1 GLY A 257 PRO A 258 0 12.26 CISPEP 2 GLY B 257 PRO B 258 0 -5.54 CISPEP 3 LEU C 193 ARG C 194 0 3.22 CISPEP 4 ARG C 194 GLY C 195 0 -29.46 CISPEP 5 GLY C 195 LEU C 196 0 -2.87 CISPEP 6 GLY C 257 PRO C 258 0 7.74 CISPEP 7 GLU C 286 ASP C 287 0 -18.15 CISPEP 8 LEU D 193 ARG D 194 0 -19.53 CISPEP 9 ARG D 194 GLY D 195 0 -16.02 CISPEP 10 GLY D 195 LEU D 196 0 22.55 CISPEP 11 GLY D 257 PRO D 258 0 5.93 CISPEP 12 GLU D 286 ASP D 287 0 10.15 CRYST1 91.188 50.960 202.599 90.00 95.51 90.00 I 1 2 1 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 0.010966 0.000000 0.001059 0.00000 SCALE2 0.000000 0.019623 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004959 0.00000