PDB Short entry for 3LE4 HEADER NUCLEAR PROTEIN 14-JAN-10 3LE4 TITLE CRYSTAL STRUCTURE OF THE DGCR8 DIMERIZATION DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MICROPROCESSOR COMPLEX SUBUNIT DGCR8; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DIMERIZATION DOMAIN (UNP RESIDUES 275 TO 353); COMPND 5 SYNONYM: DIGEORGE SYNDROME CRITICAL REGION 8; COMPND 6 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: DGCR8, C22ORF12, DGCRK6, LP4941; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS WW MOTIF, DIMERIZATION, 3D DOMAIN SWAPPING, HEME BINDING, MICRORNA KEYWDS 2 PROCESSING, HEME, IRON, METAL-BINDING, NUCLEUS, PHOSPHOPROTEIN, RNA- KEYWDS 3 BINDING, NUCLEAR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.SENTURIA,D.CASCIO,M.SAWAYA,F.GUO REVDAT 2 21-FEB-24 3LE4 1 REMARK REVDAT 1 07-JUL-10 3LE4 0 JRNL AUTH R.SENTURIA,M.FALLER,S.YIN,J.A.LOO,D.CASCIO,M.R.SAWAYA, JRNL AUTH 2 D.HWANG,R.T.CLUBB,F.GUO JRNL TITL STRUCTURE OF THE DIMERIZATION DOMAIN OF DIGEORGE CRITICAL JRNL TITL 2 REGION 8 JRNL REF PROTEIN SCI. V. 19 1354 2010 JRNL REFN ISSN 0961-8368 JRNL PMID 20506313 JRNL DOI 10.1002/PRO.414 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 7721 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.670 REMARK 3 FREE R VALUE TEST SET COUNT : 347 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 28.2542 - 2.1435 0.99 3699 198 0.1855 0.2171 REMARK 3 2 1.7600 - 1.7014 0.95 3389 149 0.1667 0.1989 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 : 0.43 REMARK 3 B_SOL : 68.55 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 : 0.009 475 REMARK 3 ANGLE : 1.327 652 REMARK 3 CHIRALITY : 0.083 68 REMARK 3 PLANARITY : 0.006 84 REMARK 3 DIHEDRAL : 13.981 174 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 3LE4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000057164. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : CRYOGENICALLY-COOLED SINGLE REMARK 200 CRYSTAL SI(111) SIDE BOUNCE REMARK 200 MONOCHROMATOR. OPTIONAL SI(311) REMARK 200 TO ACHIVE 13.474 KEV. REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7721 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 28.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 100 MM BIS REMARK 280 -TRIS PH 5.5, 25% POLYETHYLENE GLYCOL 3350, 10 MM NICOTINAMIDE REMARK 280 ADENINE DINUCLEOTIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 40.31300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 19.97600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 19.97600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 60.46950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 19.97600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 19.97600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 20.15650 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 19.97600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 19.97600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 60.46950 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 19.97600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 19.97600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 20.15650 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 40.31300 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: 2600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6550 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 39.95200 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 39.95200 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 40.31300 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 SER A 275 REMARK 465 ASP A 276 REMARK 465 GLY A 277 REMARK 465 GLU A 278 REMARK 465 THR A 279 REMARK 465 SER A 280 REMARK 465 VAL A 281 REMARK 465 GLN A 282 REMARK 465 PRO A 283 REMARK 465 MET A 284 REMARK 465 MET A 285 REMARK 465 THR A 286 REMARK 465 LYS A 287 REMARK 465 ILE A 288 REMARK 465 LYS A 289 REMARK 465 THR A 290 REMARK 465 VAL A 291 REMARK 465 LEU A 292 REMARK 465 LYS A 293 REMARK 465 SER A 294 REMARK 465 ARG A 295 REMARK 465 GLY A 296 REMARK 465 ARG A 297 REMARK 465 LEU A 353 DBREF 3LE4 A 275 353 UNP Q8WYQ5 DGCR8_HUMAN 275 353 SEQRES 1 A 79 SER ASP GLY GLU THR SER VAL GLN PRO MET MET THR LYS SEQRES 2 A 79 ILE LYS THR VAL LEU LYS SER ARG GLY ARG PRO PRO THR SEQRES 3 A 79 GLU PRO LEU PRO ASP GLY TRP ILE MET THR PHE HIS ASN SEQRES 4 A 79 SER GLY VAL PRO VAL TYR LEU HIS ARG GLU SER ARG VAL SEQRES 5 A 79 VAL THR TRP SER ARG PRO TYR PHE LEU GLY THR GLY SER SEQRES 6 A 79 ILE ARG LYS HIS ASP PRO PRO LEU SER SER ILE PRO CYS SEQRES 7 A 79 LEU FORMUL 2 HOH *36(H2 O) HELIX 1 1 PRO A 346 ILE A 350 5 5 SHEET 1 A 3 TRP A 307 PHE A 311 0 SHEET 2 A 3 PRO A 317 HIS A 321 -1 O VAL A 318 N THR A 310 SHEET 3 A 3 VAL A 326 THR A 328 -1 O VAL A 326 N HIS A 321 CRYST1 39.952 39.952 80.626 90.00 90.00 90.00 P 43 21 2 8 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 0.025030 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025030 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012403 0.00000