HEADER RNA BINDING PROTEIN 29-JUN-17 5OC5 TITLE CRYSTAL STRUCTURE OF HUMAN TRNA-DIHYDROURIDINE(20) SYNTHASE DSRBD TITLE 2 K419A-K420A MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA-DIHYDROURIDINE(20) SYNTHASE [NAD(P)+]-LIKE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DIHYDROURIDINE SYNTHASE 2,UP-REGULATED IN LUNG CANCER COMPND 5 PROTEIN 8,URLC8,TRNA-DIHYDROURIDINE SYNTHASE 2-LIKE,HDUS2; COMPND 6 EC: 1.3.1.-; 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: DUS2, DUS2L; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11D KEYWDS DOUBLE-STRANDED RNA-BINDING DOMAIN, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.BOU-NADER,L.PECQUEUR,D.HAMDANE REVDAT 4 17-JAN-24 5OC5 1 REMARK REVDAT 3 17-APR-19 5OC5 1 JRNL REVDAT 2 16-JAN-19 5OC5 1 JRNL REVDAT 1 26-DEC-18 5OC5 0 JRNL AUTH C.BOU-NADER,P.BARRAUD,L.PECQUEUR,J.PEREZ,C.VELOURS, JRNL AUTH 2 W.SHEPARD,M.FONTECAVE,C.TISNE,D.HAMDANE JRNL TITL MOLECULAR BASIS FOR TRANSFER RNA RECOGNITION BY THE JRNL TITL 2 DOUBLE-STRANDED RNA-BINDING DOMAIN OF HUMAN DIHYDROURIDINE JRNL TITL 3 SYNTHASE 2. JRNL REF NUCLEIC ACIDS RES. V. 47 3117 2019 JRNL REFN ESSN 1362-4962 JRNL PMID 30605527 JRNL DOI 10.1093/NAR/GKY1302 REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 7670 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 768 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 36.1766 - 3.2357 1.00 1402 158 0.1437 0.1926 REMARK 3 2 3.2357 - 2.5685 1.00 1397 158 0.1743 0.2294 REMARK 3 3 2.5685 - 2.2439 1.00 1365 151 0.1704 0.2596 REMARK 3 4 2.2439 - 2.0387 1.00 1396 155 0.1944 0.2577 REMARK 3 5 2.0387 - 1.8926 0.97 1342 146 0.3208 0.3746 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.015 765 REMARK 3 ANGLE : 1.138 1029 REMARK 3 CHIRALITY : 0.073 119 REMARK 3 PLANARITY : 0.008 128 REMARK 3 DIHEDRAL : 18.072 474 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5OC5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1200005555. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98011 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7680 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.893 REMARK 200 RESOLUTION RANGE LOW (A) : 36.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.290 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: 4WFT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% PEG 4K 1 M LICL 100 MM TRIS, PH REMARK 280 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 37.54500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.77250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 56.31750 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 TOTAL BURIED SURFACE AREA: 740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL 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 337 REMARK 465 THR A 338 REMARK 465 SER A 339 REMARK 465 GLU A 340 REMARK 465 GLN A 341 REMARK 465 THR A 342 REMARK 465 GLY A 343 REMARK 465 GLU A 344 REMARK 465 PRO A 345 REMARK 465 ALA A 346 REMARK 465 GLU A 347 REMARK 465 ASP A 348 REMARK 465 GLY A 442 REMARK 465 GLU A 443 REMARK 465 GLU A 444 REMARK 465 SER A 445 REMARK 465 PRO A 446 REMARK 465 SER A 447 REMARK 465 LEU A 448 REMARK 465 HIS A 449 REMARK 465 LYS A 450 REMARK 465 HIS A 451 REMARK 465 HIS A 452 REMARK 465 HIS A 453 REMARK 465 HIS A 454 REMARK 465 HIS A 455 REMARK 465 HIS A 456 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 HOH A 618 O HOH A 637 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 601 O HOH A 644 3555 2.02 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 GLU A 407 -1.44 70.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 505 DBREF 5OC5 A 338 450 UNP Q9NX74 DUS2L_HUMAN 338 450 SEQADV 5OC5 MET A 337 UNP Q9NX74 INITIATING METHIONINE SEQADV 5OC5 ALA A 419 UNP Q9NX74 LYS 419 ENGINEERED MUTATION SEQADV 5OC5 ALA A 420 UNP Q9NX74 LYS 420 ENGINEERED MUTATION SEQADV 5OC5 HIS A 451 UNP Q9NX74 EXPRESSION TAG SEQADV 5OC5 HIS A 452 UNP Q9NX74 EXPRESSION TAG SEQADV 5OC5 HIS A 453 UNP Q9NX74 EXPRESSION TAG SEQADV 5OC5 HIS A 454 UNP Q9NX74 EXPRESSION TAG SEQADV 5OC5 HIS A 455 UNP Q9NX74 EXPRESSION TAG SEQADV 5OC5 HIS A 456 UNP Q9NX74 EXPRESSION TAG SEQRES 1 A 120 MET THR SER GLU GLN THR GLY GLU PRO ALA GLU ASP THR SEQRES 2 A 120 SER GLY VAL ILE LYS MET ALA VAL LYS PHE ASP ARG ARG SEQRES 3 A 120 ALA TYR PRO ALA GLN ILE THR PRO LYS MET CYS LEU LEU SEQRES 4 A 120 GLU TRP CYS ARG ARG GLU LYS LEU ALA GLN PRO VAL TYR SEQRES 5 A 120 GLU THR VAL GLN ARG PRO LEU ASP ARG LEU PHE SER SER SEQRES 6 A 120 ILE VAL THR VAL ALA GLU GLN LYS TYR GLN SER THR LEU SEQRES 7 A 120 TRP ASP LYS SER ALA ALA LEU ALA GLU GLN ALA ALA ALA SEQRES 8 A 120 ILE VAL CYS LEU ARG SER GLN GLY LEU PRO GLU GLY ARG SEQRES 9 A 120 LEU GLY GLU GLU SER PRO SER LEU HIS LYS HIS HIS HIS SEQRES 10 A 120 HIS HIS HIS HET GOL A 501 14 HET GOL A 502 14 HET GOL A 503 14 HET CL A 504 1 HET CL A 505 1 HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 3(C3 H8 O3) FORMUL 5 CL 2(CL 1-) FORMUL 7 HOH *56(H2 O) HELIX 1 AA1 ASP A 360 TYR A 364 5 5 HELIX 2 AA2 THR A 369 GLU A 381 1 13 HELIX 3 AA3 SER A 418 GLN A 434 1 17 SHEET 1 AA1 4 VAL A 352 MET A 355 0 SHEET 2 AA1 4 GLN A 408 SER A 412 1 O GLN A 411 N ILE A 353 SHEET 3 AA1 4 PHE A 399 VAL A 405 -1 N VAL A 405 O GLN A 408 SHEET 4 AA1 4 VAL A 387 GLN A 392 -1 N GLU A 389 O ILE A 402 SITE 1 AC1 4 THR A 390 GOL A 503 HOH A 605 HOH A 633 SITE 1 AC2 4 ARG A 397 LYS A 417 HOH A 637 HOH A 654 SITE 1 AC3 3 GLN A 392 GOL A 501 HOH A 618 SITE 1 AC4 4 ARG A 361 TRP A 377 ARG A 380 SER A 418 SITE 1 AC5 2 HOH A 606 HOH A 641 CRYST1 36.170 36.170 75.090 90.00 90.00 90.00 P 41 4 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 0.027647 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027647 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013317 0.00000