HEADER RNA BINDING PROTEIN 05-APR-07 2YT4 TITLE CRYSTAL STRUCTURE OF HUMAN DGCR8 CORE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN DGCR8; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TWO DSRBDS AND C-TERMINAL DOMAIN; COMPND 5 SYNONYM: DIGEORGE SYNDROME CRITICAL REGION 8, DIGEORGE SYNDROME COMPND 6 CHROMOSOMAL REGION; 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 STRAIN: HEK293T; SOURCE 6 GENE: DGCR8, C22ORF12, DGCRK6; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS DSRBD, RNA BINDING DOMAIN, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.CHO,S.Y.SOHN REVDAT 5 13-MAR-24 2YT4 1 REMARK REVDAT 4 25-DEC-19 2YT4 1 REMARK SEQADV REVDAT 3 24-FEB-09 2YT4 1 VERSN REVDAT 2 23-OCT-07 2YT4 1 JRNL REVDAT 1 21-AUG-07 2YT4 0 JRNL AUTH S.Y.SOHN,W.J.BAE,J.J.KIM,K.H.YEOM,V.N.KIM,Y.CHO JRNL TITL CRYSTAL STRUCTURE OF HUMAN DGCR8 CORE JRNL REF NAT.STRUCT.MOL.BIOL. V. 14 847 2007 JRNL REFN ISSN 1545-9993 JRNL PMID 17704815 JRNL DOI 10.1038/NSMB1294 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 40313.930 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 82.7 REMARK 3 NUMBER OF REFLECTIONS : 5934 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 SET) : 0.214 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.600 REMARK 3 FREE R VALUE TEST SET COUNT : 332 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.015 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 49.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 545 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 45 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.048 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1564 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 39 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 16.01000 REMARK 3 B22 (A**2) : 1.20000 REMARK 3 B33 (A**2) : -17.21000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 5.56000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.31 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.39 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.33 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.430 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.460 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.950 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.970 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 50.69 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2YT4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-APR-07. REMARK 100 THE DEPOSITION ID IS D_1000027100. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98010 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8118 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07000 REMARK 200 FOR THE DATA SET : 19.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.30300 REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M SODIUM/POTASSIUM PHOSPHATE BUFFER REMARK 280 PH8.0, 0.9MM CTAB (CETYLTRIMETHYLAMMONIUM BROMIDE), 5MM DTT, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 28.75550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.99250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 28.75550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.99250 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: 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 ALA A 497 REMARK 465 PRO A 498 REMARK 465 THR A 499 REMARK 465 THR A 584 REMARK 465 SER A 585 REMARK 465 GLU A 586 REMARK 465 GLU A 587 REMARK 465 LYS A 588 REMARK 465 PRO A 589 REMARK 465 LYS A 590 REMARK 465 ASP A 591 REMARK 465 VAL A 643 REMARK 465 VAL A 644 REMARK 465 PRO A 645 REMARK 465 GLY A 646 REMARK 465 LYS A 647 REMARK 465 ASN A 648 REMARK 465 SER A 702 REMARK 465 SER A 703 REMARK 465 LYS A 704 REMARK 465 MET A 705 REMARK 465 VAL A 706 REMARK 465 LYS A 707 REMARK 465 GLN A 708 REMARK 465 GLU A 709 REMARK 465 THR A 710 REMARK 465 SER A 711 REMARK 465 ASP A 712 REMARK 465 LYS A 713 REMARK 465 SER A 714 REMARK 465 VAL A 715 REMARK 465 ILE A 716 REMARK 465 GLU A 717 REMARK 465 LEU A 718 REMARK 465 GLN A 719 REMARK 465 GLN A 720 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 SER A 490 -149.22 -108.66 REMARK 500 TYR A 553 -102.67 -116.29 REMARK 500 PHE A 580 48.67 -70.78 REMARK 500 VAL A 581 70.54 -103.32 REMARK 500 LYS A 582 3.55 58.63 REMARK 500 GLU A 594 -71.02 -42.75 REMARK 500 LEU A 595 24.09 -61.70 REMARK 500 PHE A 598 -7.28 -52.90 REMARK 500 ARG A 700 -79.15 -72.60 REMARK 500 REMARK 500 REMARK: NULL DBREF 2YT4 A 493 720 UNP Q8WYQ5 DGCR8_HUMAN 493 720 SEQADV 2YT4 GLY A 489 UNP Q8WYQ5 EXPRESSION TAG SEQADV 2YT4 SER A 490 UNP Q8WYQ5 EXPRESSION TAG SEQADV 2YT4 HIS A 491 UNP Q8WYQ5 EXPRESSION TAG SEQADV 2YT4 MET A 492 UNP Q8WYQ5 EXPRESSION TAG SEQRES 1 A 232 GLY SER HIS MET SER VAL GLN ASP ALA PRO THR LYS LYS SEQRES 2 A 232 GLU PHE VAL ILE ASN PRO ASN GLY LYS SER GLU VAL CYS SEQRES 3 A 232 ILE LEU HIS GLU TYR MET GLN ARG VAL LEU LYS VAL ARG SEQRES 4 A 232 PRO VAL TYR ASN PHE PHE GLU CYS GLU ASN PRO SER GLU SEQRES 5 A 232 PRO PHE GLY ALA SER VAL THR ILE ASP GLY VAL THR TYR SEQRES 6 A 232 GLY SER GLY THR ALA SER SER LYS LYS LEU ALA LYS ASN SEQRES 7 A 232 LYS ALA ALA ARG ALA THR LEU GLU ILE LEU ILE PRO ASP SEQRES 8 A 232 PHE VAL LYS GLN THR SER GLU GLU LYS PRO LYS ASP SER SEQRES 9 A 232 GLU GLU LEU GLU TYR PHE ASN HIS ILE SER ILE GLU ASP SEQRES 10 A 232 SER ARG VAL TYR GLU LEU THR SER LYS ALA GLY LEU LEU SEQRES 11 A 232 SER PRO TYR GLN ILE LEU HIS GLU CYS LEU LYS ARG ASN SEQRES 12 A 232 HIS GLY MET GLY ASP THR SER ILE LYS PHE GLU VAL VAL SEQRES 13 A 232 PRO GLY LYS ASN GLN LYS SER GLU TYR VAL MET ALA CYS SEQRES 14 A 232 GLY LYS HIS THR VAL ARG GLY TRP CYS LYS ASN LYS ARG SEQRES 15 A 232 VAL GLY LYS GLN LEU ALA SER GLN LYS ILE LEU GLN LEU SEQRES 16 A 232 LEU HIS PRO HIS VAL LYS ASN TRP GLY SER LEU LEU ARG SEQRES 17 A 232 MET TYR GLY ARG GLU SER SER LYS MET VAL LYS GLN GLU SEQRES 18 A 232 THR SER ASP LYS SER VAL ILE GLU LEU GLN GLN FORMUL 2 HOH *39(H2 O) HELIX 1 1 SER A 511 VAL A 523 1 13 HELIX 2 2 SER A 560 ILE A 577 1 18 HELIX 3 3 GLU A 593 ILE A 601 5 9 HELIX 4 4 ARG A 607 GLY A 616 1 10 HELIX 5 5 SER A 619 ARG A 630 1 12 HELIX 6 6 ASN A 668 HIS A 685 1 18 HELIX 7 7 ASN A 690 GLY A 699 1 10 SHEET 1 A 2 MET A 492 GLN A 495 0 SHEET 2 A 2 GLU A 502 ILE A 505 -1 O PHE A 503 N VAL A 494 SHEET 1 B 3 VAL A 529 GLU A 534 0 SHEET 2 B 3 PHE A 542 ILE A 548 -1 O SER A 545 N ASN A 531 SHEET 3 B 3 VAL A 551 ALA A 558 -1 O GLY A 556 N ALA A 544 SHEET 1 C 3 THR A 637 LYS A 640 0 SHEET 2 C 3 SER A 651 CYS A 657 -1 O ALA A 656 N SER A 638 SHEET 3 C 3 HIS A 660 CYS A 666 -1 O VAL A 662 N MET A 655 CRYST1 57.511 59.985 70.921 90.00 106.86 90.00 C 1 2 1 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 0.017388 0.000000 0.005269 0.00000 SCALE2 0.000000 0.016671 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014733 0.00000