HEADER RNA BINDING PROTEIN 27-OCT-24 9K9P TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS DCL4 DSRBD2 IN COMPLEX WITH DRB4 CTD COMPND MOL_ID: 1; COMPND 2 MOLECULE: DICER-LIKE PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.26.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DOUBLE-STRANDED RNA-BINDING PROTEIN 4; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: DSRNA-BINDING PROTEIN 4,ATDRB4; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: DCL4, AT5G20320, F5O24.210; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX6P1; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 13 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 14 ORGANISM_TAXID: 3702; SOURCE 15 GENE: DBR4, AT3G62800, F26K9.230; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PSUMO KEYWDS DCL4, DRB4, SIRNA, DICER, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.WANG,J.DU REVDAT 1 18-FEB-26 9K9P 0 JRNL AUTH C.WANG,J.DU JRNL TITL CRYSTAL STRUCTURE OF ARABIDOPSIS DCL4 DSRBD2 IN COMPLEX WITH JRNL TITL 2 DRB4 CTD JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 25421 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.910 REMARK 3 FREE R VALUE TEST SET COUNT : 3759 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 1.4400 - 1.4200 0.89 1423 121 0.2825 0.2897 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.133 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.519 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.23 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 : 0.007 1053 REMARK 3 ANGLE : 0.972 1426 REMARK 3 CHIRALITY : 0.086 155 REMARK 3 PLANARITY : 0.006 182 REMARK 3 DIHEDRAL : 6.170 137 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 9K9P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 29-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1300052860. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25450 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 44.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 0.9410 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES,PH 7.5,25% (W/V) PEG1000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 16.33150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.70600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.49250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.70600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.33150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.49250 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 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 1614 REMARK 465 PRO A 1615 REMARK 465 LEU A 1616 REMARK 465 SER B 302 REMARK 465 SER B 303 REMARK 465 GLU B 304 REMARK 465 LYS B 305 REMARK 465 LYS B 306 REMARK 465 LYS B 307 REMARK 465 LYS B 354 REMARK 465 PRO B 355 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 ASP B 344 -157.28 -130.49 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 B 456 DISTANCE = 6.19 ANGSTROMS DBREF 9K9P A 1618 1702 UNP P84634 DCL4_ARATH 1618 1702 DBREF 9K9P B 303 355 UNP Q8H1D4 DRB4_ARATH 303 355 SEQADV 9K9P GLY A 1614 UNP P84634 EXPRESSION TAG SEQADV 9K9P PRO A 1615 UNP P84634 EXPRESSION TAG SEQADV 9K9P LEU A 1616 UNP P84634 EXPRESSION TAG SEQADV 9K9P GLY A 1617 UNP P84634 EXPRESSION TAG SEQADV 9K9P SER B 302 UNP Q8H1D4 EXPRESSION TAG SEQRES 1 A 89 GLY PRO LEU GLY SER SER LYS THR ALA LYS SER LEU LEU SEQRES 2 A 89 HIS GLU THR CYS VAL ALA ASN CYS TRP LYS PRO PRO HIS SEQRES 3 A 89 PHE GLU CYS CYS GLU GLU GLU GLY PRO GLY HIS LEU LYS SEQRES 4 A 89 SER PHE VAL TYR LYS VAL ILE LEU GLU VAL GLU ASP ALA SEQRES 5 A 89 PRO ASN MET THR LEU GLU CYS TYR GLY GLU ALA ARG ALA SEQRES 6 A 89 THR LYS LYS GLY ALA ALA GLU HIS ALA ALA GLN ALA ALA SEQRES 7 A 89 ILE TRP CYS LEU LYS HIS SER GLY PHE LEU CYS SEQRES 1 B 54 SER SER GLU LYS LYS LYS LEU ILE MET GLY THR GLY HIS SEQRES 2 B 54 LEU SER ILE PRO THR GLY GLN HIS VAL VAL CYS ARG PRO SEQRES 3 B 54 TRP ASN PRO GLU ILE THR LEU PRO GLN ASP ALA GLU MET SEQRES 4 B 54 LEU PHE ARG ASP ASP LYS PHE ILE ALA TYR ARG LEU VAL SEQRES 5 B 54 LYS PRO FORMUL 3 HOH *171(H2 O) HELIX 1 AA1 THR A 1621 ASN A 1633 1 13 HELIX 2 AA2 THR A 1679 SER A 1698 1 20 SHEET 1 AA1 7 HIS A1639 GLU A1646 0 SHEET 2 AA1 7 LYS A1652 VAL A1662 -1 O SER A1653 N GLU A1645 SHEET 3 AA1 7 MET A1668 TYR A1673 -1 O CYS A1672 N VAL A1658 SHEET 4 AA1 7 GLN B 321 PRO B 327 1 O CYS B 325 N TYR A1673 SHEET 5 AA1 7 PHE B 347 ARG B 351 -1 O TYR B 350 N VAL B 324 SHEET 6 AA1 7 GLU B 339 ARG B 343 -1 N GLU B 339 O ARG B 351 SHEET 7 AA1 7 ILE B 309 MET B 310 -1 N ILE B 309 O ARG B 343 CISPEP 1 ALA A 1665 PRO A 1666 0 5.11 CRYST1 32.663 44.985 89.412 90.00 90.00 90.00 P 21 21 21 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 0.030616 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022230 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011184 0.00000 MASTER 241 0 0 2 7 0 0 6 1197 2 0 12 END