HEADER HYDROLASE 29-JAN-10 3LLM TITLE CRYSTAL STRUCTURE ANALYSIS OF A RNA HELICASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT RNA HELICASE A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: NUCLEOTIDE BINDING DOMAIN (UNP RESIDUES 329-563); COMPND 5 SYNONYM: NUCLEAR DNA HELICASE II, NDH II, DEAH BOX PROTEIN 9; COMPND 6 EC: 3.6.1.-; 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: DDX9, DHX9, LKP, NDH2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)R3 PRARE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC-BSA4 KEYWDS ALPHA-BETA-ALPHA, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS KEYWDS 2 CONSORTIUM, SGC, ACTIVATOR, ATP-BINDING, DNA-BINDING, HELICASE, KEYWDS 3 HYDROLASE, METHYLATION, NUCLEOTIDE-BINDING, NUCLEUS, PHOSPHOPROTEIN, KEYWDS 4 RNA-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR P.SCHUTZ,T.KARLBERG,R.COLLINS,C.H.ARROWSMITH,H.BERGLUND,C.BOUNTRA, AUTHOR 2 S.FLODIN,A.FLORES,S.GRASLUND,M.HAMMARSTROM,A.JOHANSSON,I.JOHANSSON, AUTHOR 3 A.KALLAS,P.KRAULIS,T.KOTENYOVA,A.KOTZSCH,N.MARKOVA,M.MOCHE, AUTHOR 4 T.K.NIELSEN,P.NORDLUND,T.NYMAN,C.PERSSON,A.K.ROOS,M.I.SIPONEN, AUTHOR 5 L.SVENSSON,A.G.THORSELL,L.TRESAUGUES,S.VAN DEN BERG,E.WAHLBERG, AUTHOR 6 J.WEIGELT,M.WELIN,M.WISNIEWSKA,H.M.SCHULER,STRUCTURAL GENOMICS AUTHOR 7 CONSORTIUM (SGC) REVDAT 4 11-AUG-10 3LLM 1 JRNL REVDAT 3 23-JUN-10 3LLM 1 JRNL REVDAT 2 02-JUN-10 3LLM 1 JRNL REVDAT 1 12-MAY-10 3LLM 0 JRNL AUTH P.SCHUTZ,E.WAHLBERG,T.KARLBERG,M.HAMMARSTROM,R.COLLINS, JRNL AUTH 2 A.FLORES,H.SCHULER JRNL TITL CRYSTAL STRUCTURE OF HUMAN RNA HELICASE A (DHX9): STRUCTURAL JRNL TITL 2 BASIS FOR UNSELECTIVE NUCLEOTIDE BASE BINDING IN A DEAD-BOX JRNL TITL 3 VARIANT PROTEIN. JRNL REF J.MOL.BIOL. V. 400 768 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20510246 JRNL DOI 10.1016/J.JMB.2010.05.046 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 98.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 26598 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) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1343 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1844 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.3950 REMARK 3 BIN FREE R VALUE SET COUNT : 82 REMARK 3 BIN FREE R VALUE : 0.4230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3679 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 67 REMARK 3 SOLVENT ATOMS : 27 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.82000 REMARK 3 B22 (A**2) : 0.82000 REMARK 3 B33 (A**2) : -1.23000 REMARK 3 B12 (A**2) : 0.41000 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): 0.368 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.263 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.197 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.989 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3826 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2556 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5216 ; 1.457 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6251 ; 0.884 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 468 ; 5.611 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;38.263 ;24.379 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 635 ;16.387 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;19.733 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 605 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4180 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 742 ; 0.001 ; 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): 2356 ; 0.659 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 930 ; 0.113 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3855 ; 1.326 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1470 ; 2.033 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1361 ; 3.428 ; 4.500 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 329 A 563 5 REMARK 3 1 B 329 B 563 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 1385 ; 0.430 ; 0.500 REMARK 3 LOOSE POSITIONAL 1 A (A): 1672 ; 0.710 ; 5.000 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1385 ; 0.630 ; 2.000 REMARK 3 LOOSE THERMAL 1 A (A**2): 1672 ; 0.700 ;10.000 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 : 1.40 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. U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3LLM COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-FEB-10. REMARK 100 THE RCSB ID CODE IS RCSB057428. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98000, 0.98020, 0.96860 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26628 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 98.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09900 REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.10 REMARK 200 R MERGE FOR SHELL (I) : 0.01000 REMARK 200 R SYM FOR SHELL (I) : 1.04100 REMARK 200 FOR SHELL : 0.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 75.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08 M SODIUM CACODYLATE, 0.16 M REMARK 280 CALCIUM ACETATE HYDRATE, 14.4 % PEG 8000, 20 % GLYCEROL, PH 6.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 94.43333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.21667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 47.21667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 94.43333 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 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 474 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 349 CD OE1 OE2 REMARK 470 GLU B 367 CD OE1 OE2 REMARK 470 GLN B 371 CG CD OE1 NE2 REMARK 470 GLU B 373 CG CD OE1 OE2 REMARK 470 GLN B 374 CD OE1 NE2 REMARK 470 HIS B 376 CG ND1 CD2 CE1 NE2 REMARK 470 GLN B 379 CD OE1 NE2 REMARK 470 GLN B 383 CG CD OE1 NE2 REMARK 470 GLU B 384 CD OE1 OE2 REMARK 470 ARG B 496 CD NE CZ NH1 NH2 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 MN MN A 1 O HOH A 19 1.60 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 CYS A 469 CB CYS A 469 SG -0.115 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 LYS A 467 -92.38 -118.45 REMARK 500 PHE A 475 -17.65 95.91 REMARK 500 PHE A 555 46.64 -107.04 REMARK 500 GLN B 374 -51.19 -128.79 REMARK 500 LYS B 467 -85.86 -102.31 REMARK 500 PHE B 475 -12.91 91.75 REMARK 500 PHE B 555 41.04 -108.50 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 MN B 2 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 17 O REMARK 620 2 HOH B 18 O 93.3 REMARK 620 3 GLU B 512 OE2 87.7 88.5 REMARK 620 4 THR B 418 OG1 92.4 171.9 97.5 REMARK 620 5 ADP B 1 O1B 87.8 88.0 174.1 86.4 REMARK 620 6 HOH B 23 O 163.9 80.9 77.3 95.2 106.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 1 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 21 O REMARK 620 2 ADP A 565 O3B 105.3 REMARK 620 3 GLU A 512 OE2 82.5 169.2 REMARK 620 4 THR A 418 OG1 86.1 87.1 86.0 REMARK 620 5 HOH A 20 O 89.9 98.7 88.5 173.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CAC A 564 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 565 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 564 DBREF 3LLM A 329 563 UNP Q08211 DHX9_HUMAN 329 563 DBREF 3LLM B 329 563 UNP Q08211 DHX9_HUMAN 329 563 SEQRES 1 A 235 VAL VAL PRO TRP SER PRO PRO GLN SER ASN TRP ASN PRO SEQRES 2 A 235 TRP THR SER SER ASN ILE ASP GLU GLY PRO LEU ALA PHE SEQRES 3 A 235 ALA THR PRO GLU GLN ILE SER MSE ASP LEU LYS ASN GLU SEQRES 4 A 235 LEU MSE TYR GLN LEU GLU GLN ASP HIS ASP LEU GLN ALA SEQRES 5 A 235 ILE LEU GLN GLU ARG GLU LEU LEU PRO VAL LYS LYS PHE SEQRES 6 A 235 GLU SER GLU ILE LEU GLU ALA ILE SER GLN ASN SER VAL SEQRES 7 A 235 VAL ILE ILE ARG GLY ALA THR GLY CYS GLY LYS THR THR SEQRES 8 A 235 GLN VAL PRO GLN PHE ILE LEU ASP ASP PHE ILE GLN ASN SEQRES 9 A 235 ASP ARG ALA ALA GLU CYS ASN ILE VAL VAL THR GLN PRO SEQRES 10 A 235 ARG ARG ILE SER ALA VAL SER VAL ALA GLU ARG VAL ALA SEQRES 11 A 235 PHE GLU ARG GLY GLU GLU PRO GLY LYS SER CYS GLY TYR SEQRES 12 A 235 SER VAL ARG PHE GLU SER ILE LEU PRO ARG PRO HIS ALA SEQRES 13 A 235 SER ILE MSE PHE CYS THR VAL GLY VAL LEU LEU ARG LYS SEQRES 14 A 235 LEU GLU ALA GLY ILE ARG GLY ILE SER HIS VAL ILE VAL SEQRES 15 A 235 ASP GLU ILE HIS GLU ARG ASP ILE ASN THR ASP PHE LEU SEQRES 16 A 235 LEU VAL VAL LEU ARG ASP VAL VAL GLN ALA TYR PRO GLU SEQRES 17 A 235 VAL ARG ILE VAL LEU MSE SER ALA THR ILE ASP THR SER SEQRES 18 A 235 MSE PHE CYS GLU TYR PHE PHE ASN CYS PRO ILE ILE GLU SEQRES 19 A 235 VAL SEQRES 1 B 235 VAL VAL PRO TRP SER PRO PRO GLN SER ASN TRP ASN PRO SEQRES 2 B 235 TRP THR SER SER ASN ILE ASP GLU GLY PRO LEU ALA PHE SEQRES 3 B 235 ALA THR PRO GLU GLN ILE SER MSE ASP LEU LYS ASN GLU SEQRES 4 B 235 LEU MSE TYR GLN LEU GLU GLN ASP HIS ASP LEU GLN ALA SEQRES 5 B 235 ILE LEU GLN GLU ARG GLU LEU LEU PRO VAL LYS LYS PHE SEQRES 6 B 235 GLU SER GLU ILE LEU GLU ALA ILE SER GLN ASN SER VAL SEQRES 7 B 235 VAL ILE ILE ARG GLY ALA THR GLY CYS GLY LYS THR THR SEQRES 8 B 235 GLN VAL PRO GLN PHE ILE LEU ASP ASP PHE ILE GLN ASN SEQRES 9 B 235 ASP ARG ALA ALA GLU CYS ASN ILE VAL VAL THR GLN PRO SEQRES 10 B 235 ARG ARG ILE SER ALA VAL SER VAL ALA GLU ARG VAL ALA SEQRES 11 B 235 PHE GLU ARG GLY GLU GLU PRO GLY LYS SER CYS GLY TYR SEQRES 12 B 235 SER VAL ARG PHE GLU SER ILE LEU PRO ARG PRO HIS ALA SEQRES 13 B 235 SER ILE MSE PHE CYS THR VAL GLY VAL LEU LEU ARG LYS SEQRES 14 B 235 LEU GLU ALA GLY ILE ARG GLY ILE SER HIS VAL ILE VAL SEQRES 15 B 235 ASP GLU ILE HIS GLU ARG ASP ILE ASN THR ASP PHE LEU SEQRES 16 B 235 LEU VAL VAL LEU ARG ASP VAL VAL GLN ALA TYR PRO GLU SEQRES 17 B 235 VAL ARG ILE VAL LEU MSE SER ALA THR ILE ASP THR SER SEQRES 18 B 235 MSE PHE CYS GLU TYR PHE PHE ASN CYS PRO ILE ILE GLU SEQRES 19 B 235 VAL MODRES 3LLM MSE A 362 MET SELENOMETHIONINE MODRES 3LLM MSE A 369 MET SELENOMETHIONINE MODRES 3LLM MSE A 487 MET SELENOMETHIONINE MODRES 3LLM MSE A 542 MET SELENOMETHIONINE MODRES 3LLM MSE A 550 MET SELENOMETHIONINE MODRES 3LLM MSE B 362 MET SELENOMETHIONINE MODRES 3LLM MSE B 369 MET SELENOMETHIONINE MODRES 3LLM MSE B 487 MET SELENOMETHIONINE MODRES 3LLM MSE B 542 MET SELENOMETHIONINE MODRES 3LLM MSE B 550 MET SELENOMETHIONINE HET MSE A 362 8 HET MSE A 369 8 HET MSE A 487 8 HET MSE A 542 8 HET MSE A 550 8 HET MSE B 362 8 HET MSE B 369 8 HET MSE B 487 8 HET MSE B 542 8 HET MSE B 550 8 HET MN A 1 1 HET CAC A 564 5 HET ADP A 565 27 HET MN B 2 1 HET ADP B 1 27 HET GOL B 564 6 HETNAM MSE SELENOMETHIONINE HETNAM MN MANGANESE (II) ION HETNAM CAC CACODYLATE ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 10(C5 H11 N O2 SE) FORMUL 3 MN 2(MN 2+) FORMUL 4 CAC C2 H6 AS O2 1- FORMUL 5 ADP 2(C10 H15 N5 O10 P2) FORMUL 8 GOL C3 H8 O3 FORMUL 9 HOH *27(H2 O) HELIX 1 1 THR A 356 ASP A 375 1 20 HELIX 2 2 ASP A 375 LEU A 387 1 13 HELIX 3 3 LEU A 388 LYS A 392 5 5 HELIX 4 4 PHE A 393 ASN A 404 1 12 HELIX 5 5 GLY A 416 ASN A 432 1 17 HELIX 6 6 ARG A 434 GLU A 437 5 4 HELIX 7 7 ARG A 446 GLU A 460 1 15 HELIX 8 8 VAL A 491 GLY A 501 1 11 HELIX 9 9 ASP A 517 TYR A 534 1 18 HELIX 10 10 THR A 548 PHE A 555 1 8 HELIX 11 11 GLY B 350 PHE B 354 5 5 HELIX 12 12 THR B 356 ASP B 375 1 20 HELIX 13 13 ASP B 375 LEU B 387 1 13 HELIX 14 14 LEU B 388 LYS B 392 5 5 HELIX 15 15 PHE B 393 ASN B 404 1 12 HELIX 16 16 GLY B 416 ASN B 432 1 17 HELIX 17 17 ARG B 434 GLU B 437 5 4 HELIX 18 18 ARG B 446 GLU B 460 1 15 HELIX 19 19 VAL B 491 GLY B 501 1 11 HELIX 20 20 ASP B 517 TYR B 534 1 18 HELIX 21 21 THR B 548 PHE B 555 1 8 SHEET 1 A 2 TRP A 339 ASN A 340 0 SHEET 2 A 2 SER A 345 ASN A 346 -1 O SER A 345 N ASN A 340 SHEET 1 B 8 GLU A 476 ILE A 478 0 SHEET 2 B 8 CYS A 469 VAL A 473 -1 N VAL A 473 O GLU A 476 SHEET 3 B 8 SER A 485 THR A 490 1 O PHE A 488 N GLY A 470 SHEET 4 B 8 ASN A 439 GLN A 444 1 N VAL A 442 O MSE A 487 SHEET 5 B 8 HIS A 507 VAL A 510 1 O ILE A 509 N THR A 443 SHEET 6 B 8 ARG A 538 SER A 543 1 O ARG A 538 N VAL A 508 SHEET 7 B 8 VAL A 406 ARG A 410 1 N ILE A 409 O LEU A 541 SHEET 8 B 8 ILE A 561 GLU A 562 1 O ILE A 561 N ILE A 408 SHEET 1 C 2 TRP B 339 ASN B 340 0 SHEET 2 C 2 SER B 345 ASN B 346 -1 O SER B 345 N ASN B 340 SHEET 1 D 8 GLU B 476 ILE B 478 0 SHEET 2 D 8 CYS B 469 VAL B 473 -1 N VAL B 473 O GLU B 476 SHEET 3 D 8 SER B 485 THR B 490 1 O ILE B 486 N GLY B 470 SHEET 4 D 8 ASN B 439 GLN B 444 1 N ILE B 440 O MSE B 487 SHEET 5 D 8 HIS B 507 VAL B 510 1 O ILE B 509 N THR B 443 SHEET 6 D 8 ARG B 538 SER B 543 1 O VAL B 540 N VAL B 510 SHEET 7 D 8 VAL B 406 ARG B 410 1 N ILE B 409 O LEU B 541 SHEET 8 D 8 ILE B 560 GLU B 562 1 O ILE B 561 N ILE B 408 LINK C SER A 361 N MSE A 362 1555 1555 1.34 LINK C MSE A 362 N ASP A 363 1555 1555 1.32 LINK C LEU A 368 N MSE A 369 1555 1555 1.33 LINK C MSE A 369 N TYR A 370 1555 1555 1.32 LINK C ILE A 486 N MSE A 487 1555 1555 1.33 LINK C MSE A 487 N PHE A 488 1555 1555 1.33 LINK C LEU A 541 N MSE A 542 1555 1555 1.32 LINK C MSE A 542 N SER A 543 1555 1555 1.33 LINK C SER A 549 N MSE A 550 1555 1555 1.32 LINK C MSE A 550 N PHE A 551 1555 1555 1.33 LINK C SER B 361 N MSE B 362 1555 1555 1.33 LINK C MSE B 362 N ASP B 363 1555 1555 1.33 LINK C LEU B 368 N MSE B 369 1555 1555 1.34 LINK C MSE B 369 N TYR B 370 1555 1555 1.33 LINK C ILE B 486 N MSE B 487 1555 1555 1.32 LINK C MSE B 487 N PHE B 488 1555 1555 1.31 LINK C LEU B 541 N MSE B 542 1555 1555 1.32 LINK C MSE B 542 N SER B 543 1555 1555 1.34 LINK C SER B 549 N MSE B 550 1555 1555 1.32 LINK C MSE B 550 N PHE B 551 1555 1555 1.33 LINK MN MN B 2 O HOH B 17 1555 1555 1.83 LINK MN MN B 2 O HOH B 18 1555 1555 1.99 LINK OE2 GLU B 512 MN MN B 2 1555 1555 2.01 LINK MN MN A 1 O HOH A 21 1555 1555 2.02 LINK OG1 THR B 418 MN MN B 2 1555 1555 2.03 LINK MN MN A 1 O3B ADP A 565 1555 1555 2.05 LINK MN MN B 2 O1B ADP B 1 1555 1555 2.07 LINK OE2 GLU A 512 MN MN A 1 1555 1555 2.16 LINK MN MN B 2 O HOH B 23 1555 1555 2.17 LINK OG1 THR A 418 MN MN A 1 1555 1555 2.18 LINK MN MN A 1 O HOH A 20 1555 1555 2.35 SITE 1 AC1 6 HOH A 19 HOH A 20 HOH A 21 THR A 418 SITE 2 AC1 6 GLU A 512 ADP A 565 SITE 1 AC2 7 ADP B 1 HOH B 17 HOH B 18 HOH B 23 SITE 2 AC2 7 THR B 418 ASP B 511 GLU B 512 SITE 1 AC3 12 MN B 2 HOH B 17 HOH B 18 THR B 413 SITE 2 AC3 12 GLY B 414 CYS B 415 GLY B 416 LYS B 417 SITE 3 AC3 12 THR B 418 THR B 419 ARG B 456 HOH B 565 SITE 1 AC4 2 ASP A 375 ASP A 377 SITE 1 AC5 14 MN A 1 HOH A 13 HOH A 19 HOH A 20 SITE 2 AC5 14 HOH A 24 THR A 413 GLY A 414 CYS A 415 SITE 3 AC5 14 GLY A 416 LYS A 417 THR A 418 THR A 419 SITE 4 AC5 14 ARG A 456 PHE B 354 SITE 1 AC6 3 GLN B 403 SER B 405 ARG B 538 CRYST1 113.700 113.700 141.650 90.00 90.00 120.00 P 32 2 1 12 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 0.008795 0.005078 0.000000 0.00000 SCALE2 0.000000 0.010156 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007060 0.00000