HEADER RNA BINDING PROTEIN 05-JAN-21 7DTJ TITLE CRYSTAL STRUCTURE OF THE RECA2 DOMAIN OF RNA HELICASE CGH-1 IN C. TITLE 2 ELEGANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT RNA HELICASE CGH-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RECA2 DOMAIN; COMPND 5 SYNONYM: CONSERVED GERMLINE HELICASE 1; COMPND 6 EC: 3.6.4.13; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 GENE: CGH-1, C07H6.5; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HELICASE, RNA BINDING, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHANG,M.Q.LV,J.J.HONG REVDAT 2 29-NOV-23 7DTJ 1 REMARK REVDAT 1 17-MAR-21 7DTJ 0 JRNL AUTH Y.ZHANG,M.LV,F.LI,M.LI,J.ZHANG,Y.SHI,J.HONG JRNL TITL STRUCTURAL AND BIOCHEMICAL INSIGHTS INTO THE RECOGNITION OF JRNL TITL 2 RNA HELICASE CGH-1 BY CAR-1 IN C. ELEGANS. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 549 135 2021 JRNL REFN ESSN 1090-2104 JRNL PMID 33676181 JRNL DOI 10.1016/J.BBRC.2021.02.119 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 9664 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 494 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 30.8860 - 3.8111 0.99 2365 121 0.1979 0.2170 REMARK 3 2 3.8111 - 3.0258 1.00 2291 125 0.2419 0.3059 REMARK 3 3 3.0258 - 2.6436 1.00 2261 113 0.2772 0.3085 REMARK 3 4 2.6436 - 2.4020 1.00 2253 135 0.2895 0.2911 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 247 THROUGH 419) REMARK 3 ORIGIN FOR THE GROUP (A): -35.3133 8.0866 6.4814 REMARK 3 T TENSOR REMARK 3 T11: 0.4712 T22: 0.3947 REMARK 3 T33: 0.4682 T12: -0.0033 REMARK 3 T13: -0.0288 T23: 0.0389 REMARK 3 L TENSOR REMARK 3 L11: 0.6446 L22: 1.7565 REMARK 3 L33: 4.0919 L12: 0.1045 REMARK 3 L13: 0.0867 L23: 0.0743 REMARK 3 S TENSOR REMARK 3 S11: 0.1247 S12: -0.0771 S13: -0.0480 REMARK 3 S21: -0.1668 S22: -0.0848 S23: -0.0834 REMARK 3 S31: -0.2836 S32: 0.1380 S33: 0.0048 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7DTJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1300020101. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-19 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 : SSRF REMARK 200 BEAMLINE : BL19U1 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9668 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.402 REMARK 200 RESOLUTION RANGE LOW (A) : 30.886 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 16.50 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.61000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.167 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: 2WAX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA ACETATE PH 5.0, 20% PEG 4000, REMARK 280 0.2M AMMONION ACETATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 20.25633 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 40.51267 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 40.51267 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 20.25633 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 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 MET A 239 REMARK 465 GLY A 240 REMARK 465 HIS A 241 REMARK 465 HIS A 242 REMARK 465 HIS A 243 REMARK 465 HIS A 244 REMARK 465 HIS A 245 REMARK 465 HIS A 246 REMARK 465 GLN A 420 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 276 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 370 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 373 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 374 CG CD1 CD2 CE1 CE2 CZ REMARK 470 HIS A 376 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 377 CG CD1 CD2 REMARK 470 ARG A 402 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 419 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 281 -77.87 -81.34 REMARK 500 TYR A 415 -5.47 -152.25 REMARK 500 ASP A 418 48.77 -98.92 REMARK 500 REMARK 500 REMARK: NULL DBREF 7DTJ A 247 420 UNP Q95YF3 CGH1_CAEEL 247 420 SEQADV 7DTJ MET A 239 UNP Q95YF3 INITIATING METHIONINE SEQADV 7DTJ GLY A 240 UNP Q95YF3 EXPRESSION TAG SEQADV 7DTJ HIS A 241 UNP Q95YF3 EXPRESSION TAG SEQADV 7DTJ HIS A 242 UNP Q95YF3 EXPRESSION TAG SEQADV 7DTJ HIS A 243 UNP Q95YF3 EXPRESSION TAG SEQADV 7DTJ HIS A 244 UNP Q95YF3 EXPRESSION TAG SEQADV 7DTJ HIS A 245 UNP Q95YF3 EXPRESSION TAG SEQADV 7DTJ HIS A 246 UNP Q95YF3 EXPRESSION TAG SEQRES 1 A 182 MET GLY HIS HIS HIS HIS HIS HIS MET GLU GLU LEU THR SEQRES 2 A 182 LEU LEU GLY VAL THR GLN TYR TYR ALA PHE VAL GLN GLU SEQRES 3 A 182 LYS GLN LYS VAL HIS CYS LEU ASN THR LEU PHE ARG LYS SEQRES 4 A 182 LEU GLN ILE ASN GLN SER ILE ILE PHE CYS ASN SER THR SEQRES 5 A 182 GLN ARG VAL GLU LEU LEU ALA LYS LYS ILE THR GLU ILE SEQRES 6 A 182 GLY TYR SER CYS TYR TYR ILE HIS SER LYS MET ALA GLN SEQRES 7 A 182 ASN HIS ARG ASN ARG VAL PHE HIS ASP PHE ARG GLN GLY SEQRES 8 A 182 ASN CYS ARG ASN LEU VAL CYS SER ASP LEU LEU THR ARG SEQRES 9 A 182 GLY ILE ASP ILE GLN ALA VAL ASN VAL VAL ILE ASN PHE SEQRES 10 A 182 ASP PHE PRO ARG ASN ALA GLU THR TYR LEU HIS ARG ILE SEQRES 11 A 182 GLY ARG SER GLY ARG PHE GLY HIS LEU GLY VAL ALA ILE SEQRES 12 A 182 ASN LEU ILE THR TYR GLU ASP ARG HIS THR LEU ARG ARG SEQRES 13 A 182 ILE GLU GLN GLU LEU ARG THR ARG ILE GLU PRO ILE PRO SEQRES 14 A 182 LYS THR VAL ASP PRO LYS LEU TYR VAL ALA ASP GLN GLN FORMUL 2 HOH *9(H2 O) HELIX 1 AA1 GLN A 263 LYS A 265 5 3 HELIX 2 AA2 GLN A 266 LEU A 278 1 13 HELIX 3 AA3 SER A 289 GLY A 304 1 16 HELIX 4 AA4 ALA A 315 GLY A 329 1 15 HELIX 5 AA5 ASN A 360 GLY A 369 1 10 HELIX 6 AA6 THR A 385 GLU A 387 5 3 HELIX 7 AA7 ASP A 388 LEU A 399 1 12 HELIX 8 AA8 ASP A 411 TYR A 415 5 5 SHEET 1 AA1 7 CYS A 307 ILE A 310 0 SHEET 2 AA1 7 ASN A 333 CYS A 336 1 O VAL A 335 N ILE A 310 SHEET 3 AA1 7 GLN A 282 PHE A 286 1 N ILE A 285 O CYS A 336 SHEET 4 AA1 7 VAL A 349 ASN A 354 1 O ILE A 353 N ILE A 284 SHEET 5 AA1 7 GLY A 378 ILE A 384 1 O ILE A 381 N ASN A 354 SHEET 6 AA1 7 VAL A 255 PHE A 261 1 N TYR A 258 O ALA A 380 SHEET 7 AA1 7 ILE A 403 PRO A 405 1 O GLU A 404 N GLN A 257 CRYST1 82.825 82.825 60.769 90.00 90.00 120.00 P 31 2 1 6 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 0.012074 0.006971 0.000000 0.00000 SCALE2 0.000000 0.013941 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016456 0.00000