HEADER HYDROLASE 25-JUN-08 3DKP TITLE HUMAN DEAD-BOX RNA-HELICASE DDX52, CONSERVED DOMAIN I IN COMPLEX WITH TITLE 2 ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE ATP-DEPENDENT RNA HELICASE DDX52; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CONSERVED DOMAIN I: RESIDUES 139-381; COMPND 5 SYNONYM: DEAD BOX PROTEIN 52, ATP-DEPENDENT RNA HELICASE ROK1-LIKE; COMPND 6 EC: 3.6.1.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: DDX52, ROK1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)GOLD PRARE2; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PNIC-BSA4 KEYWDS RNA HELICASE, DEAD, ADP, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS KEYWDS 2 CONSORTIUM, SGC, RRNA, ATP-BINDING, HYDROLASE, NUCLEOTIDE-BINDING, KEYWDS 3 NUCLEUS, PHOSPHOPROTEIN, RNA-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR L.LEHTIO,T.KARLBERG,J.ANDERSSON,C.H.ARROWSMITH,H.BERGLUND,R.COLLINS, AUTHOR 2 L.G.DAHLGREN,A.M.EDWARDS,S.FLODIN,A.FLORES,S.GRASLUND,M.HAMMARSTROM, AUTHOR 3 A.JOHANSSON,I.JOHANSSON,T.KOTENYOVA,M.MOCHE,M.E.NILSSON,P.NORDLUND, AUTHOR 4 T.NYMAN,K.OLESEN,C.PERSSON,J.SAGEMARK,A.G.THORSELL,L.TRESAUGUES, AUTHOR 5 S.VAN DEN BERG,M.WELIN,M.WISNIEWSKA,M.WIKSTROM,H.SCHUELER,STRUCTURAL AUTHOR 6 GENOMICS CONSORTIUM (SGC) REVDAT 5 30-AUG-23 3DKP 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 3DKP 1 VERSN REVDAT 3 27-OCT-10 3DKP 1 JRNL REVDAT 2 24-FEB-09 3DKP 1 VERSN REVDAT 1 12-AUG-08 3DKP 0 JRNL AUTH P.SCHUTZ,T.KARLBERG,S.VAN DEN BERG,R.COLLINS,L.LEHTIO, JRNL AUTH 2 M.HOGBOM,L.HOLMBERG-SCHIAVONE,W.TEMPEL,H.W.PARK, JRNL AUTH 3 M.HAMMARSTROM,M.MOCHE,A.G.THORSELL,H.SCHULER JRNL TITL COMPARATIVE STRUCTURAL ANALYSIS OF HUMAN DEAD-BOX RNA JRNL TITL 2 HELICASES. JRNL REF PLOS ONE V. 5 12791 2010 JRNL REFN ESSN 1932-6203 JRNL PMID 20941364 JRNL DOI 10.1371/JOURNAL.PONE.0012791 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0077 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 12804 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 674 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 939 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.2190 REMARK 3 BIN FREE R VALUE SET COUNT : 49 REMARK 3 BIN FREE R VALUE : 0.2540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1868 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 168 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 25.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.68000 REMARK 3 B22 (A**2) : 0.13000 REMARK 3 B33 (A**2) : -0.81000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.269 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.205 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.138 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.364 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1978 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2686 ; 1.414 ; 1.996 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 248 ; 5.911 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 77 ;38.382 ;23.766 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 353 ;14.985 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;15.803 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 311 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1434 ; 0.006 ; 0.021 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): 1213 ; 0.624 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1966 ; 1.190 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 765 ; 1.976 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 715 ; 3.258 ; 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 137 A 179 REMARK 3 ORIGIN FOR THE GROUP (A): 4.4545 -2.1839 3.1626 REMARK 3 T TENSOR REMARK 3 T11: 0.1113 T22: 0.1212 REMARK 3 T33: 0.0899 T12: 0.0275 REMARK 3 T13: -0.0390 T23: 0.0144 REMARK 3 L TENSOR REMARK 3 L11: 1.8483 L22: 2.3800 REMARK 3 L33: 1.9701 L12: 0.5977 REMARK 3 L13: 0.2979 L23: 1.3206 REMARK 3 S TENSOR REMARK 3 S11: -0.0687 S12: 0.3463 S13: -0.0432 REMARK 3 S21: -0.1949 S22: 0.0310 S23: 0.2173 REMARK 3 S31: 0.0895 S32: -0.0747 S33: 0.0378 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 : A 180 A 298 REMARK 3 ORIGIN FOR THE GROUP (A): 16.6361 3.8485 17.5816 REMARK 3 T TENSOR REMARK 3 T11: 0.1025 T22: 0.1308 REMARK 3 T33: 0.1006 T12: 0.0565 REMARK 3 T13: 0.0012 T23: -0.0009 REMARK 3 L TENSOR REMARK 3 L11: 1.5687 L22: 1.9152 REMARK 3 L33: 1.7262 L12: 0.7850 REMARK 3 L13: 0.4511 L23: 0.7087 REMARK 3 S TENSOR REMARK 3 S11: -0.0145 S12: 0.0120 S13: -0.0244 REMARK 3 S21: 0.0814 S22: 0.0693 S23: -0.1329 REMARK 3 S31: 0.1158 S32: 0.2710 S33: -0.0548 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 : A 299 A 378 REMARK 3 ORIGIN FOR THE GROUP (A): 5.5431 8.3133 24.5469 REMARK 3 T TENSOR REMARK 3 T11: 0.0955 T22: 0.1008 REMARK 3 T33: 0.1222 T12: 0.0393 REMARK 3 T13: 0.0604 T23: -0.0299 REMARK 3 L TENSOR REMARK 3 L11: 1.8731 L22: 2.4194 REMARK 3 L33: 2.5883 L12: 0.4758 REMARK 3 L13: 0.8787 L23: 0.6311 REMARK 3 S TENSOR REMARK 3 S11: -0.0175 S12: -0.2318 S13: 0.1231 REMARK 3 S21: 0.2528 S22: -0.1035 S23: 0.3348 REMARK 3 S31: 0.0638 S32: -0.1950 S33: 0.1210 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: NULL REMARK 4 REMARK 4 3DKP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000048158. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : SILICON (111) CHANNEL-CUT REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13480 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.650 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.68 REMARK 200 R MERGE FOR SHELL (I) : 0.37800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.610 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: PDB ENTRY 2DB3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 8000, 100 MM IMIDAZOLE, PH REMARK 280 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 19.18000 REMARK 290 SMTRY3 2 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 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 LYS A 328 REMARK 465 THR A 329 REMARK 465 ARG A 379 REMARK 465 ASN A 380 REMARK 465 SER A 381 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 GLN A 186 CD OE1 NE2 REMARK 470 ASN A 232 CG OD1 ND2 REMARK 470 LYS A 233 CE NZ REMARK 470 LYS A 281 CG CD CE NZ REMARK 470 ASP A 326 CG OD1 OD2 REMARK 470 GLU A 361 CD OE1 OE2 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 LYS A 228 -58.16 67.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 ADP A 403 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 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP A 402 O1B REMARK 620 2 HOH A 422 O 173.0 REMARK 620 3 HOH A 561 O 99.5 85.2 REMARK 620 4 HOH A 562 O 90.4 85.1 81.5 REMARK 620 5 HOH A 563 O 93.8 90.9 95.8 175.3 REMARK 620 6 HOH A 564 O 93.2 81.6 165.3 90.9 90.8 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 MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 404 DBREF 3DKP A 139 381 UNP Q9Y2R4 DDX52_HUMAN 139 381 SEQADV 3DKP SER A 137 UNP Q9Y2R4 EXPRESSION TAG SEQADV 3DKP MET A 138 UNP Q9Y2R4 EXPRESSION TAG SEQRES 1 A 245 SER MET LYS ILE ASN PHE LEU ARG ASN LYS HIS LYS ILE SEQRES 2 A 245 HIS VAL GLN GLY THR ASP LEU PRO ASP PRO ILE ALA THR SEQRES 3 A 245 PHE GLN GLN LEU ASP GLN GLU TYR LYS ILE ASN SER ARG SEQRES 4 A 245 LEU LEU GLN ASN ILE LEU ASP ALA GLY PHE GLN MET PRO SEQRES 5 A 245 THR PRO ILE GLN MET GLN ALA ILE PRO VAL MET LEU HIS SEQRES 6 A 245 GLY ARG GLU LEU LEU ALA SER ALA PRO THR GLY SER GLY SEQRES 7 A 245 LYS THR LEU ALA PHE SER ILE PRO ILE LEU MET GLN LEU SEQRES 8 A 245 LYS GLN PRO ALA ASN LYS GLY PHE ARG ALA LEU ILE ILE SEQRES 9 A 245 SER PRO THR ARG GLU LEU ALA SER GLN ILE HIS ARG GLU SEQRES 10 A 245 LEU ILE LYS ILE SER GLU GLY THR GLY PHE ARG ILE HIS SEQRES 11 A 245 MET ILE HIS LYS ALA ALA VAL ALA ALA LYS LYS PHE GLY SEQRES 12 A 245 PRO LYS SER SER LYS LYS PHE ASP ILE LEU VAL THR THR SEQRES 13 A 245 PRO ASN ARG LEU ILE TYR LEU LEU LYS GLN ASP PRO PRO SEQRES 14 A 245 GLY ILE ASP LEU ALA SER VAL GLU TRP LEU VAL VAL ASP SEQRES 15 A 245 GLU SER ASP LYS LEU PHE GLU ASP GLY LYS THR GLY PHE SEQRES 16 A 245 ARG ASP GLN LEU ALA SER ILE PHE LEU ALA CYS THR SER SEQRES 17 A 245 HIS LYS VAL ARG ARG ALA MET PHE SER ALA THR PHE ALA SEQRES 18 A 245 TYR ASP VAL GLU GLN TRP CYS LYS LEU ASN LEU ASP ASN SEQRES 19 A 245 VAL ILE SER VAL SER ILE GLY ALA ARG ASN SER HET MG A 401 1 HET ADP A 402 27 HET ADP A 403 9 HET GOL A 404 6 HETNAM MG MAGNESIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MG MG 2+ FORMUL 3 ADP 2(C10 H15 N5 O10 P2) FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *168(H2 O) HELIX 1 1 SER A 137 HIS A 147 1 11 HELIX 2 2 THR A 162 LYS A 171 1 10 HELIX 3 3 ASN A 173 ALA A 183 1 11 HELIX 4 4 THR A 189 HIS A 201 1 13 HELIX 5 5 GLY A 214 LYS A 228 1 15 HELIX 6 6 THR A 243 SER A 258 1 16 HELIX 7 7 HIS A 269 LYS A 276 1 8 HELIX 8 8 THR A 292 GLN A 302 1 11 HELIX 9 9 GLU A 319 GLY A 327 1 9 HELIX 10 10 GLY A 330 CYS A 342 1 13 HELIX 11 11 ALA A 357 LEU A 368 1 12 SHEET 1 A 8 ILE A 149 GLN A 152 0 SHEET 2 A 8 ILE A 372 ILE A 376 -1 O SER A 375 N HIS A 150 SHEET 3 A 8 LEU A 205 SER A 208 1 N LEU A 206 O VAL A 374 SHEET 4 A 8 ARG A 348 SER A 353 1 O MET A 351 N LEU A 205 SHEET 5 A 8 TRP A 314 VAL A 317 1 N VAL A 317 O PHE A 352 SHEET 6 A 8 ALA A 237 ILE A 240 1 N ILE A 240 O VAL A 316 SHEET 7 A 8 ILE A 288 THR A 291 1 O LEU A 289 N ILE A 239 SHEET 8 A 8 ILE A 265 HIS A 266 1 N HIS A 266 O VAL A 290 LINK MG MG A 401 O1B ADP A 402 1555 1555 1.99 LINK MG MG A 401 O HOH A 422 1555 1555 2.18 LINK MG MG A 401 O HOH A 561 1555 1555 2.21 LINK MG MG A 401 O HOH A 562 1555 1555 1.97 LINK MG MG A 401 O HOH A 563 1555 1555 2.09 LINK MG MG A 401 O HOH A 564 1555 1555 1.95 CISPEP 1 ASP A 303 PRO A 304 0 3.37 SITE 1 AC1 5 HOH A 422 HOH A 561 HOH A 562 HOH A 563 SITE 2 AC1 5 HOH A 564 SITE 1 AC2 17 PHE A 185 MET A 187 GLN A 192 PRO A 210 SITE 2 AC2 17 THR A 211 GLY A 212 SER A 213 GLY A 214 SITE 3 AC2 17 LYS A 215 THR A 216 HOH A 416 HOH A 421 SITE 4 AC2 17 HOH A 435 HOH A 534 HOH A 562 HOH A 563 SITE 5 AC2 17 HOH A 564 SITE 1 AC3 6 ARG A 244 HIS A 269 LYS A 270 ARG A 295 SITE 2 AC3 6 TYR A 358 HOH A 493 SITE 1 AC4 5 THR A 189 PRO A 190 GLY A 212 SER A 213 SITE 2 AC4 5 HIS A 345 CRYST1 40.630 38.360 73.840 90.00 90.37 90.00 P 1 21 1 2 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 0.024612 0.000000 0.000160 0.00000 SCALE2 0.000000 0.026069 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013543 0.00000