10 20 30 40 50 60 70 80 1OXJ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA BINDING PROTEIN 02-APR-03 1OXJ
TITLE CRYSTAL STRUCTURE OF THE SMAUG RNA BINDING DOMAIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-BINDING PROTEIN SMAUG; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RNA BINDING DOMAIN, SAM DOMAIN; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: SMG; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET 15B
KEYWDS SAM DOMAIN, PHAT DOMAIN, RNA-BINDING PROTEIN, RNA BINDING KEYWDS 2 PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR J.B.GREEN,C.D.GARDNER,R.P.WHARTON,A.K.AGGARWAL
REVDAT 2 24-FEB-09 1OXJ 1 VERSN REVDAT 1 08-JUL-03 1OXJ 0
JRNL AUTH J.B.GREEN,C.D.GARDNER,R.P.WHARTON,A.K.AGGARWAL JRNL TITL RNA RECOGNITION VIA THE SAM DOMAIN OF SMAUG. JRNL REF MOL.CELL V. 11 1537 2003 JRNL REFN ISSN 1097-2765 JRNL PMID 12820967 JRNL DOI 10.1016/S1097-2765(03)00178-3
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.8 REMARK 3 NUMBER OF REFLECTIONS : 18277 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) : 0.229 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1257 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 70.27 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3613 REMARK 3 BIN FREE R VALUE : 0.3761 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 107 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1355 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 163 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.26 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) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.30 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.01 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.55 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.70 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.407 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1OXJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-APR-03. REMARK 100 THE RCSB ID CODE IS RCSB018774.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-01; 13-APR-01 REMARK 200 TEMPERATURE (KELVIN) : 170; 170 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; NSLS REMARK 200 BEAMLINE : 19-ID; X25 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.94207, 0.97941, 0.97927; REMARK 200 0.9188 REMARK 200 MONOCHROMATOR : SI (111); SI(111) REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : SBC-2; BRANDEIS - B4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19192 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 34.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 50.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM ACETATE, PH 8.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 64.66000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 37.33147 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 11.04167 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 64.66000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 37.33147 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 11.04167 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 64.66000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 37.33147 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 11.04167 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 74.66294 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 22.08333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 74.66294 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 22.08333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 74.66294 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 22.08333 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 GLY A 592 REMARK 465 THR A 593 REMARK 465 LYS A 764
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 LYS A 618 -73.85 -19.69 REMARK 500 GLU A 693 28.09 -74.75 REMARK 500 REMARK 500 REMARK: NULL
REMARK 999 REMARK 999 SEQUENCE REMARK 999 HIS TAG IS REMOVED LEAVING THE NON-SMG SEQUENCE REMARK 999 GTHM ON THE N-TERMINAL END.
DBREF 1OXJ A 596 764 UNP Q23972 SMG_DROME 596 764
SEQADV 1OXJ GLY A 592 UNP Q23972 SEE REMARK 999 SEQADV 1OXJ THR A 593 UNP Q23972 SEE REMARK 999 SEQADV 1OXJ HIS A 594 UNP Q23972 SEE REMARK 999 SEQADV 1OXJ MET A 595 UNP Q23972 SEE REMARK 999
SEQRES 1 A 173 GLY THR HIS MET VAL GLY MET SER GLY ILE GLY LEU TRP SEQRES 2 A 173 LEU LYS SER LEU ARG LEU HIS LYS TYR ILE GLU LEU PHE SEQRES 3 A 173 LYS ASN MET THR TYR GLU GLU MET LEU LEU ILE THR GLU SEQRES 4 A 173 ASP PHE LEU GLN SER VAL GLY VAL THR LYS GLY ALA SER SEQRES 5 A 173 HIS LYS LEU ALA LEU CYS ILE ASP LYS LEU LYS GLU ARG SEQRES 6 A 173 ALA ASN ILE LEU ASN ARG VAL GLU GLN GLU LEU LEU SER SEQRES 7 A 173 GLY GLN MET GLU LEU SER THR ALA VAL GLU GLU LEU THR SEQRES 8 A 173 ASN ILE VAL LEU THR PRO MET LYS PRO LEU GLU SER PRO SEQRES 9 A 173 GLY PRO PRO GLU GLU ASN ILE GLY LEU ARG PHE LEU LYS SEQRES 10 A 173 VAL ILE ASP ILE VAL THR ASN THR LEU GLN GLN ASP PRO SEQRES 11 A 173 TYR ALA VAL GLN ASP ASP GLU THR LEU GLY VAL LEU MET SEQRES 12 A 173 TRP ILE LEU ASP ARG SER ILE HIS ASN GLU ALA PHE MET SEQRES 13 A 173 ASN HIS ALA SER GLN LEU LYS ASP LEU LYS PHE LYS LEU SEQRES 14 A 173 SER LYS MET LYS
FORMUL 2 HOH *163(H2 O)
HELIX 1 1 GLY A 600 LEU A 608 1 9 HELIX 2 2 ARG A 609 ARG A 609 5 1 HELIX 3 3 LEU A 610 LYS A 618 5 9 HELIX 4 4 THR A 621 LEU A 626 1 6 HELIX 5 5 THR A 629 VAL A 636 1 8 HELIX 6 6 THR A 639 SER A 669 1 31 HELIX 7 7 GLU A 673 ASN A 683 1 11 HELIX 8 8 PRO A 697 GLU A 700 5 4 HELIX 9 9 ASN A 701 GLN A 719 1 19 HELIX 10 10 TYR A 722 GLN A 725 5 4 HELIX 11 11 ASP A 726 HIS A 742 1 17 HELIX 12 12 ASN A 743 ASN A 748 5 6 HELIX 13 13 HIS A 749 LYS A 762 1 14
CRYST1 129.320 129.320 33.125 90.00 90.00 120.00 H 3 9
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 0.007733 0.004465 0.000000 0.00000
SCALE2 0.000000 0.008929 0.000000 0.00000
SCALE3 0.000000 0.000000 0.030189 0.00000