HEADER RNA BINDING PROTEIN 05-AUG-05 2ALE TITLE CRYSTAL STRUCTURE OF YEAST RNA SPLICING FACTOR SNU13P COMPND MOL_ID: 1; COMPND 2 MOLECULE: NHP2/L7AE FAMILY PROTEIN YEL026W; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SNU13; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21D KEYWDS SPLICING, RNA, YEAST, HIS-TAG, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.C.DOBBYN,P.A.MCEWAN,J.BELLA,R.T.O'KEEFE REVDAT 4 23-AUG-23 2ALE 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 2ALE 1 VERSN REVDAT 2 04-SEP-07 2ALE 1 JRNL REVDAT 1 03-OCT-06 2ALE 0 JRNL AUTH H.C.DOBBYN,P.A.MCEWAN,A.KRAUSE,L.NOVAK-FRAZER,J.BELLA, JRNL AUTH 2 R.T.O'KEEFE JRNL TITL ANALYSIS OF PRE-MRNA AND PRE-RRNA PROCESSING FACTOR SNU13P JRNL TITL 2 STRUCTURE AND MUTANTS. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 360 857 2007 JRNL REFN ISSN 0006-291X JRNL PMID 17631273 JRNL DOI 10.1016/J.BBRC.2007.06.163 REMARK 2 REMARK 2 RESOLUTION. 1.80 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1097129.430 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 14341 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) : 0.223 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1450 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2112 REMARK 3 BIN R VALUE (WORKING SET) : 0.3170 REMARK 3 BIN FREE R VALUE : 0.3410 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 215 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1007 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.07000 REMARK 3 B22 (A**2) : 5.07000 REMARK 3 B33 (A**2) : -10.14000 REMARK 3 B12 (A**2) : 2.16000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.25 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) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.27 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.270 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) : 2.310 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.380 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.620 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 21.04 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_H2O.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN_H2O.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP. REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ALE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034030. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : CONFOCAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14642 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 40.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 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) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.15 REMARK 200 R MERGE FOR SHELL (I) : 0.32600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1E7K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE, 0.1 M SODIUM REMARK 280 CACODYLATE, 30% PEG 8K, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 17.76767 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 35.53533 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.53533 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 17.76767 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 MG MG A1001 LIES ON A SPECIAL POSITION. 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 HIS A 133 REMARK 465 HIS A 134 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 ASN A 105 93.78 -170.45 REMARK 500 GLU A 128 -173.64 67.98 REMARK 500 HIS A 129 112.37 42.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 73 OD2 REMARK 620 2 ASP A 73 OD1 52.5 REMARK 620 3 ASP A 73 OD1 151.6 99.2 REMARK 620 4 ASP A 73 OD2 155.9 151.6 52.5 REMARK 620 5 HIS A 132 NE2 86.4 114.6 107.3 80.4 REMARK 620 6 HIS A 132 NE2 80.4 107.3 114.6 86.4 113.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1E7K RELATED DB: PDB REMARK 900 15.5K HUMAN HOMOLOGUE DBREF 2ALE A 1 126 UNP P39990 NHPX_YEAST 1 126 SEQADV 2ALE LEU A 127 UNP P39990 CLONING ARTIFACT SEQADV 2ALE GLU A 128 UNP P39990 CLONING ARTIFACT SEQADV 2ALE HIS A 129 UNP P39990 EXPRESSION TAG SEQADV 2ALE HIS A 130 UNP P39990 EXPRESSION TAG SEQADV 2ALE HIS A 131 UNP P39990 EXPRESSION TAG SEQADV 2ALE HIS A 132 UNP P39990 EXPRESSION TAG SEQADV 2ALE HIS A 133 UNP P39990 EXPRESSION TAG SEQADV 2ALE HIS A 134 UNP P39990 EXPRESSION TAG SEQRES 1 A 134 MET SER ALA PRO ASN PRO LYS ALA PHE PRO LEU ALA ASP SEQRES 2 A 134 ALA ALA LEU THR GLN GLN ILE LEU ASP VAL VAL GLN GLN SEQRES 3 A 134 ALA ALA ASN LEU ARG GLN LEU LYS LYS GLY ALA ASN GLU SEQRES 4 A 134 ALA THR LYS THR LEU ASN ARG GLY ILE SER GLU PHE ILE SEQRES 5 A 134 ILE MET ALA ALA ASP CYS GLU PRO ILE GLU ILE LEU LEU SEQRES 6 A 134 HIS LEU PRO LEU LEU CYS GLU ASP LYS ASN VAL PRO TYR SEQRES 7 A 134 VAL PHE VAL PRO SER ARG VAL ALA LEU GLY ARG ALA CYS SEQRES 8 A 134 GLY VAL SER ARG PRO VAL ILE ALA ALA SER ILE THR THR SEQRES 9 A 134 ASN ASP ALA SER ALA ILE LYS THR GLN ILE TYR ALA VAL SEQRES 10 A 134 LYS ASP LYS ILE GLU THR LEU LEU ILE LEU GLU HIS HIS SEQRES 11 A 134 HIS HIS HIS HIS HET MG A1001 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG MG 2+ FORMUL 3 HOH *66(H2 O) HELIX 1 1 ASP A 13 LEU A 30 1 18 HELIX 2 2 GLY A 36 GLY A 47 1 12 HELIX 3 3 PRO A 60 LEU A 64 5 5 HELIX 4 4 LEU A 65 ASN A 75 1 11 HELIX 5 5 SER A 83 CYS A 91 1 9 HELIX 6 6 ILE A 110 LEU A 127 1 18 SHEET 1 A 4 LEU A 33 LYS A 35 0 SHEET 2 A 4 ALA A 99 THR A 103 -1 O SER A 101 N LYS A 34 SHEET 3 A 4 SER A 49 ALA A 55 -1 N GLU A 50 O ILE A 102 SHEET 4 A 4 TYR A 78 VAL A 81 1 O VAL A 81 N MET A 54 LINK OD2 ASP A 73 MG MG A1001 1555 1555 2.60 LINK OD1 ASP A 73 MG MG A1001 1555 1555 2.33 LINK OD1 ASP A 73 MG MG A1001 6765 1555 2.33 LINK OD2 ASP A 73 MG MG A1001 6765 1555 2.60 LINK NE2 HIS A 132 MG MG A1001 1555 1555 2.23 LINK NE2 HIS A 132 MG MG A1001 6765 1555 2.23 CISPEP 1 PHE A 9 PRO A 10 0 -0.36 CISPEP 2 GLU A 59 PRO A 60 0 -0.35 SITE 1 AC1 2 ASP A 73 HIS A 132 CRYST1 70.330 70.330 53.303 90.00 90.00 120.00 P 31 2 1 6 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 0.014219 0.008209 0.000000 0.00000 SCALE2 0.000000 0.016418 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018761 0.00000