HEADER DNA BINDING PROTEIN/DNA/RNA 13-FEB-17 5USN TITLE CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE POT1PC BOUND TO TITLE 2 SSRNA/SSDNA CHIMERA (RGRGRUTACGGT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTECTION OF TELOMERES PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 199-339; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 1-3R_9MER DNA/RNA (5'-R(*GP*GP*U)-D(P*TP*AP*CP*GP*GP*T)- COMPND 9 3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 3 ORGANISM_COMMON: FISSION YEAST; SOURCE 4 ORGANISM_TAXID: 4896; SOURCE 5 GENE: POT1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 11 ORGANISM_TAXID: 4896 KEYWDS TELOMERES, OB-FOLD, DNA BINDING, DNA BINDING PROTEIN-DNA-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.R.LLOYD,D.S.WUTTKE REVDAT 3 04-OCT-23 5USN 1 LINK REVDAT 2 16-MAY-18 5USN 1 JRNL REVDAT 1 18-APR-18 5USN 0 JRNL AUTH N.R.LLOYD,D.S.WUTTKE JRNL TITL DISCRIMINATION AGAINST RNA BACKBONES BY A SSDNA BINDING JRNL TITL 2 PROTEIN. JRNL REF STRUCTURE V. 26 722 2018 JRNL REFN ISSN 1878-4186 JRNL PMID 29681468 JRNL DOI 10.1016/J.STR.2018.03.016 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 44.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 13388 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1334 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 44.3514 - 4.0925 1.00 1309 145 0.1952 0.2090 REMARK 3 2 4.0925 - 3.2486 1.00 1250 140 0.1565 0.2077 REMARK 3 3 3.2486 - 2.8381 1.00 1225 133 0.1789 0.1945 REMARK 3 4 2.8381 - 2.5786 0.99 1205 134 0.1922 0.2188 REMARK 3 5 2.5786 - 2.3938 0.99 1189 132 0.1836 0.2447 REMARK 3 6 2.3938 - 2.2527 0.98 1205 131 0.1883 0.2480 REMARK 3 7 2.2527 - 2.1399 0.99 1165 128 0.1799 0.2472 REMARK 3 8 2.1399 - 2.0467 0.99 1189 132 0.1857 0.2583 REMARK 3 9 2.0467 - 1.9679 0.98 1162 130 0.1905 0.2372 REMARK 3 10 1.9679 - 1.9000 0.97 1155 129 0.2218 0.2764 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.480 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 : 0.008 1436 REMARK 3 ANGLE : 1.104 1980 REMARK 3 CHIRALITY : 0.047 207 REMARK 3 PLANARITY : 0.004 220 REMARK 3 DIHEDRAL : 17.397 549 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 5USN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1000226433. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM, MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 0.5.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13518 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 59.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.27300 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: PHASER 2.6.0, PHASER REMARK 200 STARTING MODEL: 4HIK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS, 0.2 MM SODIUM FORMATE, REMARK 280 15% PEG 4000, PH 8.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K 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 20.82000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.04000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.90000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.04000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.82000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.90000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 HZ3 LYS A 25 O HOH A 209 1.59 REMARK 500 O HOH A 243 O HOH B 229 1.82 REMARK 500 O HOH A 297 O HOH A 317 1.82 REMARK 500 O HOH A 243 O HOH B 207 1.87 REMARK 500 O HOH B 214 O HOH B 228 1.92 REMARK 500 O HOH A 282 O HOH B 208 1.95 REMARK 500 O HOH A 205 O HOH A 333 1.95 REMARK 500 O HOH A 235 O HOH A 298 2.05 REMARK 500 O HOH B 202 O HOH B 215 2.07 REMARK 500 O HOH A 209 O HOH A 243 2.07 REMARK 500 OP2 U B 3 O HOH B 201 2.07 REMARK 500 O HOH A 211 O HOH A 316 2.13 REMARK 500 OP2 DT B 4 O HOH B 202 2.16 REMARK 500 O HOH A 248 O HOH A 336 2.18 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 311 O HOH A 314 2555 1.65 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 TRP A 58 107.63 -46.71 REMARK 500 ASP A 73 -123.94 50.61 REMARK 500 TYR A 82 -55.79 -135.33 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 NA B 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 126 O REMARK 620 2 HOH A 277 O 29.7 REMARK 620 3 G B 1 O2' 23.8 6.6 REMARK 620 4 HOH B 204 O 28.6 4.6 4.9 REMARK 620 5 HOH B 222 O 27.5 2.6 4.1 3.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5USB RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH G1R 9MER REMARK 900 RELATED ID: 5USO RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH 7-9R 9MER DBREF 5USN A 3 143 UNP O13988 POT1_SCHPO 199 339 DBREF 5USN B 1 9 PDB 5USN 5USN 1 9 SEQADV 5USN ASP A 3 UNP O13988 VAL 199 ENGINEERED MUTATION SEQRES 1 A 141 ASP SER PHE SER LEU LEU SER GLN ILE THR PRO HIS GLN SEQRES 2 A 141 ARG CYS SER PHE TYR ALA GLN VAL ILE LYS THR TRP TYR SEQRES 3 A 141 SER ASP LYS ASN PHE THR LEU TYR VAL THR ASP TYR THR SEQRES 4 A 141 GLU ASN GLU LEU PHE PHE PRO MET SER PRO TYR THR SER SEQRES 5 A 141 SER SER ARG TRP ARG GLY PRO PHE GLY ARG PHE SER ILE SEQRES 6 A 141 ARG CYS ILE LEU TRP ASP GLU HIS ASP PHE TYR CYS ARG SEQRES 7 A 141 ASN TYR ILE LYS GLU GLY ASP TYR VAL VAL MET LYS ASN SEQRES 8 A 141 VAL ARG THR LYS ILE ASP HIS LEU GLY TYR LEU GLU CYS SEQRES 9 A 141 ILE LEU HIS GLY ASP SER ALA LYS ARG TYR ASN MET SER SEQRES 10 A 141 ILE GLU LYS VAL ASP SER GLU GLU PRO GLU LEU ASN GLU SEQRES 11 A 141 ILE LYS SER ARG LYS ARG LEU TYR VAL GLN ASN SEQRES 1 B 9 G G U DT DA DC DG DG DT HET NA B 101 1 HETNAM NA SODIUM ION FORMUL 3 NA NA 1+ FORMUL 4 HOH *175(H2 O) HELIX 1 AA1 LEU A 7 ILE A 11 5 5 HELIX 2 AA2 TRP A 72 ARG A 80 1 9 HELIX 3 AA3 GLU A 127 GLU A 129 5 3 HELIX 4 AA4 LEU A 130 ASN A 143 1 14 SHEET 1 AA1 7 SER A 119 VAL A 123 0 SHEET 2 AA1 7 TYR A 88 ILE A 98 -1 N TYR A 88 O VAL A 123 SHEET 3 AA1 7 LEU A 104 LEU A 108 -1 O ILE A 107 N ARG A 95 SHEET 4 AA1 7 ILE A 67 LEU A 71 1 N ILE A 70 O LEU A 108 SHEET 5 AA1 7 PHE A 33 THR A 38 -1 N LEU A 35 O CYS A 69 SHEET 6 AA1 7 ARG A 16 TYR A 28 -1 N GLN A 22 O THR A 38 SHEET 7 AA1 7 TYR A 88 ILE A 98 -1 O VAL A 89 N ALA A 21 LINK O GLU A 126 NA NA B 101 1555 1455 2.94 LINK O HOH A 277 NA NA B 101 1655 1555 2.35 LINK O2' G B 1 NA NA B 101 1555 1555 2.66 LINK NA NA B 101 O HOH B 204 1555 1555 2.81 LINK NA NA B 101 O HOH B 222 1555 1555 2.59 SITE 1 AC1 5 GLU A 126 HOH A 277 G B 1 HOH B 204 SITE 2 AC1 5 HOH B 222 CRYST1 41.640 59.800 66.080 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 0.024015 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016722 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015133 0.00000