HEADER TRANSCRIPTION 05-MAR-14 4PQZ TITLE CRYSTAL STRUCTURE OF SWT1 C-TERMINAL DOMAIN FROM YEAST COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL PROTEIN SWT1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN (UNP RESIDUES 312-458); COMPND 5 SYNONYM: SYNTHETICALLY LETHAL WITH TREX PROTEIN 1; COMPND 6 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 GENE: SWT1, YOR166C, O3595; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS HEPN LIKE FOLD, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR S.X.PENG,Z.Q.GAO,Q.S.LIU,Y.H.DONG REVDAT 5 06-NOV-24 4PQZ 1 REMARK REVDAT 4 03-APR-24 4PQZ 1 SEQADV REVDAT 3 22-NOV-17 4PQZ 1 REMARK REVDAT 2 24-DEC-14 4PQZ 1 JRNL REVDAT 1 03-DEC-14 4PQZ 0 JRNL AUTH S.PENG,K.ZHOU,W.WANG,Z.GAO,Y.DONG,Q.LIU JRNL TITL HIGH-RESOLUTION CRYSTAL STRUCTURE REVEALS A HEPN DOMAIN AT JRNL TITL 2 THE C-TERMINAL REGION OF S. CEREVISIAE RNA ENDONUCLEASE JRNL TITL 3 SWT1. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 453 826 2014 JRNL REFN ISSN 0006-291X JRNL PMID 25450355 JRNL DOI 10.1016/J.BBRC.2014.10.040 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_869) 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 8407 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.690 REMARK 3 FREE R VALUE TEST SET COUNT : 394 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 28.3245 - 3.3163 0.93 2651 139 0.2005 0.2400 REMARK 3 2 3.3163 - 2.6328 1.00 2717 131 0.2159 0.2975 REMARK 3 3 2.6328 - 2.3000 0.98 2645 124 0.2671 0.3409 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 44.56 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.510 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.990 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) : -7.73370 REMARK 3 B22 (A**2) : -7.73370 REMARK 3 B33 (A**2) : 15.46740 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.009 1180 REMARK 3 ANGLE : 1.141 1595 REMARK 3 CHIRALITY : 0.084 175 REMARK 3 PLANARITY : 0.004 198 REMARK 3 DIHEDRAL : 15.950 427 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 4PQZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000085113. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BSRF REMARK 200 BEAMLINE : 3W1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8407 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 98.9 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 61.8900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.40 REMARK 200 R MERGE FOR SHELL (I) : 0.39500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.990 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: SEMET DERIVATIVE OF L379M MUTANT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE, 2 M SODIUM REMARK 280 FORMATE, PH 4.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 56.64467 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 28.32233 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 28.32233 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 56.64467 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 MET A 292 REMARK 465 GLY A 293 REMARK 465 SER A 294 REMARK 465 SER A 295 REMARK 465 HIS A 296 REMARK 465 HIS A 297 REMARK 465 HIS A 298 REMARK 465 HIS A 299 REMARK 465 HIS A 300 REMARK 465 HIS A 301 REMARK 465 SER A 302 REMARK 465 SER A 303 REMARK 465 GLY A 304 REMARK 465 GLU A 305 REMARK 465 ASN A 306 REMARK 465 LEU A 307 REMARK 465 TYR A 308 REMARK 465 PHE A 309 REMARK 465 GLN A 310 REMARK 465 GLY A 311 REMARK 465 SER A 312 REMARK 465 TYR A 313 REMARK 465 ALA A 314 REMARK 465 HIS A 315 REMARK 465 ILE A 316 REMARK 465 PRO A 317 REMARK 465 GLY A 318 REMARK 465 ILE A 319 REMARK 465 GLU A 320 REMARK 465 THR A 321 REMARK 465 PRO A 322 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 ND2 ASN A 454 O HOH A 515 2.19 REMARK 500 OE1 GLU A 387 O HOH A 522 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 O HOH A 509 O HOH A 509 5555 1.99 REMARK 500 OD1 ASN A 414 O HOH A 513 5555 2.17 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 CYS A 391 37.93 -91.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP A 365 LYS A 366 35.56 REMARK 500 REMARK 500 REMARK: NULL DBREF 4PQZ A 312 458 UNP Q12104 SWT1_YEAST 312 458 SEQADV 4PQZ MET A 292 UNP Q12104 EXPRESSION TAG SEQADV 4PQZ GLY A 293 UNP Q12104 EXPRESSION TAG SEQADV 4PQZ SER A 294 UNP Q12104 EXPRESSION TAG SEQADV 4PQZ SER A 295 UNP Q12104 EXPRESSION TAG SEQADV 4PQZ HIS A 296 UNP Q12104 EXPRESSION TAG SEQADV 4PQZ HIS A 297 UNP Q12104 EXPRESSION TAG SEQADV 4PQZ HIS A 298 UNP Q12104 EXPRESSION TAG SEQADV 4PQZ HIS A 299 UNP Q12104 EXPRESSION TAG SEQADV 4PQZ HIS A 300 UNP Q12104 EXPRESSION TAG SEQADV 4PQZ HIS A 301 UNP Q12104 EXPRESSION TAG SEQADV 4PQZ SER A 302 UNP Q12104 EXPRESSION TAG SEQADV 4PQZ SER A 303 UNP Q12104 EXPRESSION TAG SEQADV 4PQZ GLY A 304 UNP Q12104 EXPRESSION TAG SEQADV 4PQZ GLU A 305 UNP Q12104 EXPRESSION TAG SEQADV 4PQZ ASN A 306 UNP Q12104 EXPRESSION TAG SEQADV 4PQZ LEU A 307 UNP Q12104 EXPRESSION TAG SEQADV 4PQZ TYR A 308 UNP Q12104 EXPRESSION TAG SEQADV 4PQZ PHE A 309 UNP Q12104 EXPRESSION TAG SEQADV 4PQZ GLN A 310 UNP Q12104 EXPRESSION TAG SEQADV 4PQZ GLY A 311 UNP Q12104 EXPRESSION TAG SEQRES 1 A 167 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 167 GLU ASN LEU TYR PHE GLN GLY SER TYR ALA HIS ILE PRO SEQRES 3 A 167 GLY ILE GLU THR PRO PRO LEU GLN PHE ASP LYS VAL SER SEQRES 4 A 167 GLN ASN VAL PHE GLU GLN VAL LYS GLU THR ILE PHE PHE SEQRES 5 A 167 ALA ILE ASP HIS THR LEU ARG LYS GLU TYR GLY GLU ASP SEQRES 6 A 167 ILE GLY PHE ILE ASP TYR ASN PRO ASP LYS LEU THR THR SEQRES 7 A 167 ILE GLU ASN ALA SER ASN TYR ILE TYR LEU PHE TRP VAL SEQRES 8 A 167 SER VAL PHE SER GLU LEU PHE THR CYS SER LYS ILE LYS SEQRES 9 A 167 LYS ASN GLU TRP LYS SER LEU PRO THR VAL LEU LYS SER SEQRES 10 A 167 LYS PRO THR ASN LEU ASN ASP LEU ARG THR PHE GLU GLN SEQRES 11 A 167 PHE TRP GLU THR VAL LEU HIS PHE LEU PHE SER LYS PHE SEQRES 12 A 167 THR ASN GLU GLU LYS GLN SER LEU GLU LYS GLN ILE HIS SEQRES 13 A 167 GLU TRP LYS THR SER ILE ASN ALA ILE SER THR FORMUL 2 HOH *25(H2 O) HELIX 1 1 GLN A 325 GLY A 354 1 30 HELIX 2 2 GLU A 355 GLY A 358 5 4 HELIX 3 3 THR A 369 PHE A 380 1 12 HELIX 4 4 VAL A 384 PHE A 389 1 6 HELIX 5 5 LYS A 395 LYS A 400 5 6 HELIX 6 6 PRO A 403 SER A 408 1 6 HELIX 7 7 ASN A 412 PHE A 431 1 20 HELIX 8 8 THR A 435 ALA A 455 1 21 SSBOND 1 CYS A 391 CYS A 391 1555 6555 2.06 CRYST1 61.518 61.518 84.967 90.00 90.00 120.00 P 32 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 0.016255 0.009385 0.000000 0.00000 SCALE2 0.000000 0.018770 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011769 0.00000