HEADER RNA BINDING PROTEIN 19-DEC-14 4RZA TITLE PRE-MRNA-SPLICING FACTOR 38A AS 1-205 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRE-MRNA-SPLICING FACTOR 38A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-205; COMPND 5 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: PRPF38A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETM11 KEYWDS RNA-SPLICING, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.SCHUETZE,A.ULRICH,M.C.WAHL REVDAT 3 28-FEB-24 4RZA 1 REMARK REVDAT 2 21-SEP-16 4RZA 1 REMARK REVDAT 1 02-DEC-15 4RZA 0 JRNL AUTH T.SCHUETZE,L.APELT,A.ULRICH,G.WEBER,N.BARTLICK,U.STELZL, JRNL AUTH 2 M.C.WAHL JRNL TITL THE N-TERMINAL DOMAIN OF THE UNUSUAL SR PROTEIN HPRP38 IS AN JRNL TITL 2 INTERACTION HUB IN THE SPLICEOSOME JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 14297 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 716 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 44.9800 - 3.2476 1.00 2842 150 0.1546 0.1833 REMARK 3 2 3.2476 - 2.5778 1.00 2729 144 0.1618 0.2227 REMARK 3 3 2.5778 - 2.2519 1.00 2689 141 0.1497 0.1981 REMARK 3 4 2.2519 - 2.0460 1.00 2664 140 0.1512 0.2506 REMARK 3 5 2.0460 - 1.9000 0.99 2662 141 0.1859 0.2686 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.520 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 : 0.006 1554 REMARK 3 ANGLE : 0.992 2102 REMARK 3 CHIRALITY : 0.041 229 REMARK 3 PLANARITY : 0.004 270 REMARK 3 DIHEDRAL : 14.869 616 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 4RZA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000087981. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.895 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14297 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 44.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 5.0, 16% PEG 3350, 0.2 M REMARK 280 (NH4)2SO4, AND 5% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K 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 21.30600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.40250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.71650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.40250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.30600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.71650 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 ARG A 180 REMARK 465 VAL A 181 REMARK 465 SER A 182 REMARK 465 ALA A 183 REMARK 465 LEU A 184 REMARK 465 GLU A 185 REMARK 465 GLU A 186 REMARK 465 ASP A 187 REMARK 465 MET A 188 REMARK 465 ASP A 189 REMARK 465 ASP A 190 REMARK 465 VAL A 191 REMARK 465 GLU A 192 REMARK 465 SER A 193 REMARK 465 SER A 194 REMARK 465 GLU A 195 REMARK 465 GLU A 196 REMARK 465 GLU A 197 REMARK 465 GLU A 198 REMARK 465 GLU A 199 REMARK 465 GLU A 200 REMARK 465 ASP A 201 REMARK 465 GLU A 202 REMARK 465 LYS A 203 REMARK 465 LEU A 204 REMARK 465 GLU A 205 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 311 O HOH A 359 2.16 REMARK 500 O HOH A 384 O HOH A 387 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 ILE A 65 61.07 35.77 REMARK 500 GLN A 81 70.95 50.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4RZ9 RELATED DB: PDB DBREF 4RZA A 1 205 UNP Q8NAV1 PR38A_HUMAN 1 205 SEQRES 1 A 205 MET ALA ASN ARG THR VAL LYS ASP ALA HIS SER ILE HIS SEQRES 2 A 205 GLY THR ASN PRO GLN TYR LEU VAL GLU LYS ILE ILE ARG SEQRES 3 A 205 THR ARG ILE TYR GLU SER LYS TYR TRP LYS GLU GLU CYS SEQRES 4 A 205 PHE GLY LEU THR ALA GLU LEU VAL VAL ASP LYS ALA MET SEQRES 5 A 205 GLU LEU ARG PHE VAL GLY GLY VAL TYR GLY GLY ASN ILE SEQRES 6 A 205 LYS PRO THR PRO PHE LEU CYS LEU THR LEU LYS MET LEU SEQRES 7 A 205 GLN ILE GLN PRO GLU LYS ASP ILE ILE VAL GLU PHE ILE SEQRES 8 A 205 LYS ASN GLU ASP PHE LYS TYR VAL ARG MET LEU GLY ALA SEQRES 9 A 205 LEU TYR MET ARG LEU THR GLY THR ALA ILE ASP CYS TYR SEQRES 10 A 205 LYS TYR LEU GLU PRO LEU TYR ASN ASP TYR ARG LYS ILE SEQRES 11 A 205 LYS SER GLN ASN ARG ASN GLY GLU PHE GLU LEU MET HIS SEQRES 12 A 205 VAL ASP GLU PHE ILE ASP GLU LEU LEU HIS SER GLU ARG SEQRES 13 A 205 VAL CYS ASP ILE ILE LEU PRO ARG LEU GLN LYS ARG TYR SEQRES 14 A 205 VAL LEU GLU GLU ALA GLU GLN LEU GLU PRO ARG VAL SER SEQRES 15 A 205 ALA LEU GLU GLU ASP MET ASP ASP VAL GLU SER SER GLU SEQRES 16 A 205 GLU GLU GLU GLU GLU ASP GLU LYS LEU GLU FORMUL 2 HOH *98(H2 O) HELIX 1 1 ASN A 16 VAL A 21 5 6 HELIX 2 2 GLU A 22 SER A 32 1 11 HELIX 3 3 SER A 32 CYS A 39 1 8 HELIX 4 4 THR A 43 GLU A 45 5 3 HELIX 5 5 LEU A 46 MET A 52 1 7 HELIX 6 6 THR A 68 GLN A 81 1 14 HELIX 7 7 GLU A 83 ASN A 93 1 11 HELIX 8 8 PHE A 96 GLY A 111 1 16 HELIX 9 9 THR A 112 GLU A 121 1 10 HELIX 10 10 PRO A 122 ASP A 126 5 5 HELIX 11 11 VAL A 144 SER A 154 1 11 SHEET 1 A 3 VAL A 57 GLY A 58 0 SHEET 2 A 3 LYS A 129 GLN A 133 1 O LYS A 131 N VAL A 57 SHEET 3 A 3 PHE A 139 HIS A 143 -1 O GLU A 140 N SER A 132 SHEET 1 B 2 VAL A 60 TYR A 61 0 SHEET 2 B 2 LYS A 66 PRO A 67 -1 O LYS A 66 N TYR A 61 SHEET 1 C 2 ARG A 156 VAL A 157 0 SHEET 2 C 2 ILE A 160 ILE A 161 -1 O ILE A 160 N VAL A 157 CRYST1 42.612 59.433 68.805 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 0.023468 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016826 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014534 0.00000