PDB Short entry for 2WAY HEADER HYDROLASE 18-FEB-09 2WAY TITLE STRUCTURE OF THE HUMAN DDX6 C-TERMINAL DOMAIN IN COMPLEX WITH AN EDC3- TITLE 2 FDF PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT RNA HELICASE DDX6; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, RESIDUES 296-483; COMPND 5 SYNONYM: HUMAN DDX6, DEAD BOX PROTEIN 6, ATP-DEPENDENT RNA HELICASE COMPND 6 P54, ONCOGENE RCK; COMPND 7 EC: 3.6.1.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: ENHANCER OF MRNA-DECAPPING PROTEIN 3; COMPND 11 CHAIN: B, D; COMPND 12 FRAGMENT: FDF PEPTIDE, RESIDUES 192-228; COMPND 13 SYNONYM: HUMAN EDC3, LSM16 HOMOLOG, YJEF DOMAIN-CONTAINING PROTEIN 1, COMPND 14 YJEF N-TERMINAL DOMAIN-CONTAINING PROTEIN 2, YJEF_N2, HYJEF_N2; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PRSFDUET-1; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PRSFDUET-1 KEYWDS DEAD-BOX PROTEIN, NUCLEOTIDE-BINDING, P54, RCK, MIRNA, P-BODIES, KEYWDS 2 HELICASE, DECAPPING, RNA-BINDING, PROTO-ONCOGENE, PHOSPHOPROTEIN, KEYWDS 3 CHROMOSOMAL REARRANGEMENT, ATP-DEPENDENT RNA HELICASE, HYDROLASE, KEYWDS 4 CYTOPLASM, MRNA DECAY, ATP-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR F.TRITSCHLER,O.WEICHENRIEDER REVDAT 2 13-DEC-23 2WAY 1 REMARK REVDAT 1 24-MAR-09 2WAY 0 JRNL AUTH F.TRITSCHLER,J.E.BRAUN,A.EULALIO,V.TRUFFAULT,E.IZAURRALDE, JRNL AUTH 2 O.WEICHENRIEDER JRNL TITL STRUCTURAL BASIS FOR THE MUTUALLY EXCLUSIVE ANCHORING OF P JRNL TITL 2 BODY COMPONENTS EDC3 AND TRAL TO THE DEAD BOX PROTEIN JRNL TITL 3 DDX6/ME31B. JRNL REF MOL.CELL V. 33 661 2009 JRNL REFN ISSN 1097-2765 JRNL PMID 19285948 JRNL DOI 10.1016/J.MOLCEL.2009.02.014 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0066 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 17392 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) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 944 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1278 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.12 REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.3290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2952 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 111 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.69000 REMARK 3 B22 (A**2) : -0.72000 REMARK 3 B33 (A**2) : 1.41000 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): 0.391 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.275 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.927 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.875 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3024 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4072 ; 1.777 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 353 ; 7.182 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 160 ;39.705 ;24.250 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 531 ;16.569 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;16.690 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 457 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2268 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1791 ; 0.938 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2898 ; 1.761 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1233 ; 2.665 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1174 ; 4.233 ; 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 : NULL 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.RESIDUES A 383-387, A 413-419, A 461-472, B 192-198, B REMARK 3 225-228, C 296, C 383-389, C 413-419, C 463-472, D 192-195, D REMARK 3 226--228 ARE DISORDERED REMARK 4 REMARK 4 2WAY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1290038828. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : SI(111)MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17392 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 45.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.5000 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) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.36000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.200 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: PDB ENTRY 1S2M REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.04 M KH2PO4, 16% PEG 8000, 20% REMARK 280 GLYCEROL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 23.46000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.15500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.23000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.15500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.46000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.23000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 GLY A 280 REMARK 465 PRO A 281 REMARK 465 GLN A 282 REMARK 465 ASP A 283 REMARK 465 PRO A 284 REMARK 465 TYR A 285 REMARK 465 GLU A 286 REMARK 465 ILE A 287 REMARK 465 ASN A 288 REMARK 465 LEU A 289 REMARK 465 MET A 290 REMARK 465 GLU A 291 REMARK 465 GLU A 292 REMARK 465 LEU A 293 REMARK 465 THR A 294 REMARK 465 LEU A 295 REMARK 465 PHE A 383 REMARK 465 THR A 384 REMARK 465 ARG A 385 REMARK 465 GLY A 386 REMARK 465 ILE A 387 REMARK 465 ARG A 413 REMARK 465 SER A 414 REMARK 465 GLY A 415 REMARK 465 ARG A 416 REMARK 465 PHE A 417 REMARK 465 GLY A 418 REMARK 465 HIS A 419 REMARK 465 GLU A 461 REMARK 465 TYR A 462 REMARK 465 HIS A 463 REMARK 465 SER A 464 REMARK 465 GLU A 465 REMARK 465 PRO A 466 REMARK 465 VAL A 467 REMARK 465 GLU A 468 REMARK 465 ASP A 469 REMARK 465 GLU A 470 REMARK 465 LYS A 471 REMARK 465 PRO A 472 REMARK 465 GLY B 185 REMARK 465 PRO B 186 REMARK 465 HIS B 187 REMARK 465 MET B 188 REMARK 465 ALA B 189 REMARK 465 ASP B 190 REMARK 465 LEU B 191 REMARK 465 PHE B 192 REMARK 465 GLY B 193 REMARK 465 ASP B 194 REMARK 465 ASP B 195 REMARK 465 ILE B 196 REMARK 465 GLU B 197 REMARK 465 GLU B 198 REMARK 465 TYR B 225 REMARK 465 GLU B 226 REMARK 465 ARG B 227 REMARK 465 ARG B 228 REMARK 465 GLY C 280 REMARK 465 PRO C 281 REMARK 465 GLN C 282 REMARK 465 ASP C 283 REMARK 465 PRO C 284 REMARK 465 TYR C 285 REMARK 465 GLU C 286 REMARK 465 ILE C 287 REMARK 465 ASN C 288 REMARK 465 LEU C 289 REMARK 465 MET C 290 REMARK 465 GLU C 291 REMARK 465 GLU C 292 REMARK 465 LEU C 293 REMARK 465 THR C 294 REMARK 465 LEU C 295 REMARK 465 LYS C 296 REMARK 465 PHE C 383 REMARK 465 THR C 384 REMARK 465 ARG C 385 REMARK 465 GLY C 386 REMARK 465 ILE C 387 REMARK 465 ASP C 388 REMARK 465 ILE C 389 REMARK 465 ARG C 413 REMARK 465 SER C 414 REMARK 465 GLY C 415 REMARK 465 ARG C 416 REMARK 465 PHE C 417 REMARK 465 GLY C 418 REMARK 465 HIS C 419 REMARK 465 HIS C 463 REMARK 465 SER C 464 REMARK 465 GLU C 465 REMARK 465 PRO C 466 REMARK 465 VAL C 467 REMARK 465 GLU C 468 REMARK 465 ASP C 469 REMARK 465 GLU C 470 REMARK 465 LYS C 471 REMARK 465 PRO C 472 REMARK 465 GLY D 185 REMARK 465 PRO D 186 REMARK 465 HIS D 187 REMARK 465 MET D 188 REMARK 465 ALA D 189 REMARK 465 ASP D 190 REMARK 465 LEU D 191 REMARK 465 PHE D 192 REMARK 465 GLY D 193 REMARK 465 ASP D 194 REMARK 465 ASP D 195 REMARK 465 GLU D 226 REMARK 465 ARG D 227 REMARK 465 ARG D 228 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 MET A 357 CG - SD - CE ANGL. DEV. = -9.8 DEGREES REMARK 500 LEU A 422 CA - CB - CG ANGL. DEV. = 15.1 DEGREES REMARK 500 ARG C 375 CG - CD - NE ANGL. DEV. = -14.1 DEGREES REMARK 500 ARG C 375 NE - CZ - NH2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG C 410 NE - CZ - NH1 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 CYS A 350 114.74 -168.68 REMARK 500 LYS A 356 55.51 -95.31 REMARK 500 LYS A 455 -21.12 -39.99 REMARK 500 TYR A 458 -3.80 -152.46 REMARK 500 PRO B 200 124.00 -37.19 REMARK 500 LYS C 356 56.36 -95.58 REMARK 500 TYR C 458 -15.48 -145.61 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 381 LEU A 382 147.86 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 C2056 DISTANCE = 6.08 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 1463 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1461 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1462 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1463 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VC8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE LSM DOMAIN OF HUMAN EDC3 (ENHANCER OF REMARK 900 DECAPPING 3) REMARK 900 RELATED ID: 1VEC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF RCK/P54, AHUMAN DEAD- REMARK 900 BOX PROTEIN REMARK 900 RELATED ID: 2WAX RELATED DB: PDB REMARK 900 STRUCTURE OF THE HUMAN DDX6 C-TERMINAL DOMAIN IN COMPLEX WITH AN REMARK 900 EDC3-FDF PEPTIDE DBREF 2WAY A 280 284 PDB 2WAY 2WAY 280 284 DBREF 2WAY A 285 472 UNP P26196 DDX6_HUMAN 296 483 DBREF 2WAY B 185 191 PDB 2WAY 2WAY 185 191 DBREF 2WAY B 192 228 UNP Q96F86 EDC3_HUMAN 192 228 DBREF 2WAY C 280 284 PDB 2WAY 2WAY 280 284 DBREF 2WAY C 285 472 UNP P26196 DDX6_HUMAN 296 483 DBREF 2WAY D 185 191 PDB 2WAY 2WAY 185 191 DBREF 2WAY D 192 228 UNP Q96F86 EDC3_HUMAN 192 228 SEQRES 1 A 193 GLY PRO GLN ASP PRO TYR GLU ILE ASN LEU MET GLU GLU SEQRES 2 A 193 LEU THR LEU LYS GLY VAL THR GLN TYR TYR ALA TYR VAL SEQRES 3 A 193 THR GLU ARG GLN LYS VAL HIS CYS LEU ASN THR LEU PHE SEQRES 4 A 193 SER ARG LEU GLN ILE ASN GLN SER ILE ILE PHE CYS ASN SEQRES 5 A 193 SER SER GLN ARG VAL GLU LEU LEU ALA LYS LYS ILE SER SEQRES 6 A 193 GLN LEU GLY TYR SER CYS PHE TYR ILE HIS ALA LYS MET SEQRES 7 A 193 ARG GLN GLU HIS ARG ASN ARG VAL PHE HIS ASP PHE ARG SEQRES 8 A 193 ASN GLY LEU CYS ARG ASN LEU VAL CYS THR ASP LEU PHE SEQRES 9 A 193 THR ARG GLY ILE ASP ILE GLN ALA VAL ASN VAL VAL ILE SEQRES 10 A 193 ASN PHE ASP PHE PRO LYS LEU ALA GLU THR TYR LEU HIS SEQRES 11 A 193 ARG ILE GLY ARG SER GLY ARG PHE GLY HIS LEU GLY LEU SEQRES 12 A 193 ALA ILE ASN LEU ILE THR TYR ASP ASP ARG PHE ASN LEU SEQRES 13 A 193 LYS SER ILE GLU GLU GLN LEU GLY THR GLU ILE LYS PRO SEQRES 14 A 193 ILE PRO SER ASN ILE ASP LYS SER LEU TYR VAL ALA GLU SEQRES 15 A 193 TYR HIS SER GLU PRO VAL GLU ASP GLU LYS PRO SEQRES 1 B 44 GLY PRO HIS MET ALA ASP LEU PHE GLY ASP ASP ILE GLU SEQRES 2 B 44 GLU ILE PRO ASP THR ASP PHE ASP PHE GLU GLY ASN LEU SEQRES 3 B 44 ALA LEU PHE ASP LYS ALA ALA VAL PHE GLU GLU ILE ASP SEQRES 4 B 44 THR TYR GLU ARG ARG SEQRES 1 C 193 GLY PRO GLN ASP PRO TYR GLU ILE ASN LEU MET GLU GLU SEQRES 2 C 193 LEU THR LEU LYS GLY VAL THR GLN TYR TYR ALA TYR VAL SEQRES 3 C 193 THR GLU ARG GLN LYS VAL HIS CYS LEU ASN THR LEU PHE SEQRES 4 C 193 SER ARG LEU GLN ILE ASN GLN SER ILE ILE PHE CYS ASN SEQRES 5 C 193 SER SER GLN ARG VAL GLU LEU LEU ALA LYS LYS ILE SER SEQRES 6 C 193 GLN LEU GLY TYR SER CYS PHE TYR ILE HIS ALA LYS MET SEQRES 7 C 193 ARG GLN GLU HIS ARG ASN ARG VAL PHE HIS ASP PHE ARG SEQRES 8 C 193 ASN GLY LEU CYS ARG ASN LEU VAL CYS THR ASP LEU PHE SEQRES 9 C 193 THR ARG GLY ILE ASP ILE GLN ALA VAL ASN VAL VAL ILE SEQRES 10 C 193 ASN PHE ASP PHE PRO LYS LEU ALA GLU THR TYR LEU HIS SEQRES 11 C 193 ARG ILE GLY ARG SER GLY ARG PHE GLY HIS LEU GLY LEU SEQRES 12 C 193 ALA ILE ASN LEU ILE THR TYR ASP ASP ARG PHE ASN LEU SEQRES 13 C 193 LYS SER ILE GLU GLU GLN LEU GLY THR GLU ILE LYS PRO SEQRES 14 C 193 ILE PRO SER ASN ILE ASP LYS SER LEU TYR VAL ALA GLU SEQRES 15 C 193 TYR HIS SER GLU PRO VAL GLU ASP GLU LYS PRO SEQRES 1 D 44 GLY PRO HIS MET ALA ASP LEU PHE GLY ASP ASP ILE GLU SEQRES 2 D 44 GLU ILE PRO ASP THR ASP PHE ASP PHE GLU GLY ASN LEU SEQRES 3 D 44 ALA LEU PHE ASP LYS ALA ALA VAL PHE GLU GLU ILE ASP SEQRES 4 D 44 THR TYR GLU ARG ARG HET GOL A1461 6 HET GOL A1462 6 HET GOL A1463 6 HET GOL C1463 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 GOL 4(C3 H8 O3) FORMUL 9 HOH *111(H2 O) HELIX 1 1 THR A 306 ARG A 308 5 3 HELIX 2 2 GLN A 309 LEU A 321 1 13 HELIX 3 3 SER A 332 LEU A 346 1 15 HELIX 4 4 ARG A 358 ASN A 371 1 14 HELIX 5 5 LEU A 403 GLY A 412 1 10 HELIX 6 6 THR A 428 ASP A 430 5 3 HELIX 7 7 ASP A 431 GLY A 443 1 13 HELIX 8 8 ASP A 454 TYR A 458 5 5 HELIX 9 9 ASP B 205 LEU B 212 1 8 HELIX 10 10 ASP B 214 THR B 224 1 11 HELIX 11 11 THR C 306 ARG C 308 5 3 HELIX 12 12 GLN C 309 LEU C 321 1 13 HELIX 13 13 SER C 332 LEU C 346 1 15 HELIX 14 14 ARG C 358 ASN C 371 1 14 HELIX 15 15 LEU C 403 GLY C 412 1 10 HELIX 16 16 THR C 428 ASP C 430 5 3 HELIX 17 17 ASP C 431 GLY C 443 1 13 HELIX 18 18 ASP C 454 TYR C 458 5 5 HELIX 19 19 ASP D 205 ALA D 211 1 7 HELIX 20 20 ASP D 214 TYR D 225 1 12 SHEET 1 AA 7 PHE A 351 ILE A 353 0 SHEET 2 AA 7 ASN A 376 CYS A 379 1 O ASN A 376 N PHE A 351 SHEET 3 AA 7 GLN A 325 PHE A 329 1 O SER A 326 N LEU A 377 SHEET 4 AA 7 VAL A 392 ASN A 397 1 N ASN A 393 O GLN A 325 SHEET 5 AA 7 GLY A 421 ILE A 427 1 O LEU A 422 N VAL A 395 SHEET 6 AA 7 VAL A 298 TYR A 304 1 O THR A 299 N ALA A 423 SHEET 7 AA 7 LYS A 447 PRO A 448 1 O LYS A 447 N TYR A 302 SHEET 1 CA 7 PHE C 351 TYR C 352 0 SHEET 2 CA 7 ASN C 376 CYS C 379 1 O ASN C 376 N PHE C 351 SHEET 3 CA 7 GLN C 325 PHE C 329 1 O SER C 326 N LEU C 377 SHEET 4 CA 7 VAL C 392 ASN C 397 1 N ASN C 393 O GLN C 325 SHEET 5 CA 7 GLY C 421 ILE C 427 1 O LEU C 422 N VAL C 395 SHEET 6 CA 7 VAL C 298 TYR C 304 1 O THR C 299 N ALA C 423 SHEET 7 CA 7 LYS C 447 PRO C 448 1 O LYS C 447 N TYR C 302 SITE 1 AC1 7 GLN A 334 GLU A 337 PHE C 318 ILE C 323 SITE 2 AC1 7 TYR C 348 ARG C 375 ASN C 376 SITE 1 AC2 5 PHE A 351 TYR A 352 MET A 357 HIS A 361 SITE 2 AC2 5 VAL A 365 SITE 1 AC3 8 GLU A 307 LYS A 310 ASN A 331 ASP A 399 SITE 2 AC3 8 LYS A 402 ASP A 431 HOH A2037 HOH A2038 SITE 1 AC4 6 PHE A 318 TYR A 348 ARG A 375 ASN A 376 SITE 2 AC4 6 GLN C 334 GLU C 337 CRYST1 46.920 80.460 110.310 90.00 90.00 90.00 P 21 21 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 0.021313 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012429 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009065 0.00000