PDB Short entry for 4RZ9 HEADER RNA BINDING PROTEIN 19-DEC-14 4RZ9 TITLE PRE-MRNA-SPLICING FACTOR 38A AS 1-179 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRE-MRNA-SPLICING FACTOR 38A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 27-179; 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,G.WEBER,M.C.WAHL REVDAT 1 02-DEC-15 4RZ9 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. 1.28 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- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 46008 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.128 REMARK 3 R VALUE (WORKING SET) : 0.126 REMARK 3 FREE R VALUE : 0.150 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 2318 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 19.0400 - 3.2859 0.99 2724 147 0.1435 0.1594 REMARK 3 2 3.2859 - 2.6103 1.00 2639 137 0.1329 0.1301 REMARK 3 3 2.6103 - 2.2809 1.00 2603 139 0.1151 0.1298 REMARK 3 4 2.2809 - 2.0727 1.00 2584 133 0.1035 0.1505 REMARK 3 5 2.0727 - 1.9243 1.00 2595 139 0.1014 0.1327 REMARK 3 6 1.9243 - 1.8109 1.00 2564 136 0.1055 0.1318 REMARK 3 7 1.8109 - 1.7203 1.00 2567 132 0.1049 0.1391 REMARK 3 8 1.7203 - 1.6454 1.00 2574 132 0.1025 0.1463 REMARK 3 9 1.6454 - 1.5821 1.00 2534 135 0.1016 0.1528 REMARK 3 10 1.5821 - 1.5276 1.00 2560 126 0.1119 0.1492 REMARK 3 11 1.5276 - 1.4798 1.00 2548 135 0.1234 0.1492 REMARK 3 12 1.4798 - 1.4375 1.00 2526 136 0.1320 0.1612 REMARK 3 13 1.4375 - 1.3997 1.00 2546 127 0.1440 0.1609 REMARK 3 14 1.3997 - 1.3656 1.00 2528 149 0.1613 0.2010 REMARK 3 15 1.3656 - 1.3345 1.00 2527 139 0.1733 0.2004 REMARK 3 16 1.3345 - 1.3061 1.00 2540 130 0.1784 0.2444 REMARK 3 17 1.3061 - 1.2800 1.00 2531 146 0.1952 0.2041 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.560 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 : 0.011 1806 REMARK 3 ANGLE : 1.354 2499 REMARK 3 CHIRALITY : 0.084 277 REMARK 3 PLANARITY : 0.006 329 REMARK 3 DIHEDRAL : 14.185 781 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 4RZ9 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 RCSB ID CODE IS RCSB087980. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-SEP-11 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL 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 : 46008 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.280 REMARK 200 RESOLUTION RANGE LOW (A) : 19.040 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) : 0.05500 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) : 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 <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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.5, AND 15% (W/V) PEG REMARK 280 400, VAPOR DIFFUSION, SITTING DROP, 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 20.94300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.85500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.92400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.85500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.94300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.92400 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 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 OE1 GLN A 18 HE21 GLN A 79 1.59 REMARK 500 O HOH A 376 O HOH A 401 1.96 REMARK 500 O HOH A 230 O HOH A 312 2.02 REMARK 500 O HOH A 394 O HOH A 407 2.03 REMARK 500 O HOH A 389 O HOH A 413 2.07 REMARK 500 O HOH A 371 O HOH A 382 2.09 REMARK 500 OD1 ASN A 136 O HOH A 338 2.15 REMARK 500 O HOH A 312 O HOH A 401 2.17 REMARK 500 O HOH A 213 O HOH A 376 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD1 ASN A 64 O HOH A 288 3745 2.02 REMARK 500 OE2 GLU A 45 O HOH A 232 4466 2.06 REMARK 500 OE2 GLU A 83 O HOH A 351 4466 2.07 REMARK 500 O HOH A 232 O HOH A 286 4566 2.11 REMARK 500 ND2 ASN A 125 O HOH A 332 3755 2.12 REMARK 500 ND2 ASN A 125 O HOH A 212 3755 2.14 REMARK 500 OE2 GLU A 155 O HOH A 340 2664 2.15 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 ASN A 64 30.21 -99.49 REMARK 500 ILE A 65 73.91 38.06 REMARK 500 GLN A 81 70.11 55.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 362 DISTANCE = 5.51 ANGSTROMS REMARK 525 HOH A 412 DISTANCE = 6.54 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4RZA RELATED DB: PDB DBREF 4RZ9 A 1 179 UNP Q8NAV1 PR38A_HUMAN 1 179 SEQRES 1 A 179 MET ALA ASN ARG THR VAL LYS ASP ALA HIS SER ILE HIS SEQRES 2 A 179 GLY THR ASN PRO GLN TYR LEU VAL GLU LYS ILE ILE ARG SEQRES 3 A 179 THR ARG ILE TYR GLU SER LYS TYR TRP LYS GLU GLU CYS SEQRES 4 A 179 PHE GLY LEU THR ALA GLU LEU VAL VAL ASP LYS ALA MET SEQRES 5 A 179 GLU LEU ARG PHE VAL GLY GLY VAL TYR GLY GLY ASN ILE SEQRES 6 A 179 LYS PRO THR PRO PHE LEU CYS LEU THR LEU LYS MET LEU SEQRES 7 A 179 GLN ILE GLN PRO GLU LYS ASP ILE ILE VAL GLU PHE ILE SEQRES 8 A 179 LYS ASN GLU ASP PHE LYS TYR VAL ARG MET LEU GLY ALA SEQRES 9 A 179 LEU TYR MET ARG LEU THR GLY THR ALA ILE ASP CYS TYR SEQRES 10 A 179 LYS TYR LEU GLU PRO LEU TYR ASN ASP TYR ARG LYS ILE SEQRES 11 A 179 LYS SER GLN ASN ARG ASN GLY GLU PHE GLU LEU MET HIS SEQRES 12 A 179 VAL ASP GLU PHE ILE ASP GLU LEU LEU HIS SER GLU ARG SEQRES 13 A 179 VAL CYS ASP ILE ILE LEU PRO ARG LEU GLN LYS ARG TYR SEQRES 14 A 179 VAL LEU GLU GLU ALA GLU GLN LEU GLU PRO FORMUL 2 HOH *247(H2 O) HELIX 1 1 ASN A 16 VAL A 21 5 6 HELIX 2 2 GLU A 22 GLU A 31 1 10 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 HELIX 12 12 LYS A 167 ALA A 174 1 8 SHEET 1 A 3 VAL A 57 GLY A 58 0 SHEET 2 A 3 LYS A 129 GLN A 133 1 O GLN A 133 N VAL A 57 SHEET 3 A 3 PHE A 139 HIS A 143 -1 O MET A 142 N ILE A 130 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 41.886 61.848 67.710 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 0.023874 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016169 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014769 0.00000