HEADER DNA BINDING PROTEIN 11-OCT-12 4HIK TITLE CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE POT1PC BOUND TO SSDNA TITLE 2 (GGTTACGGT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTECTION OF TELOMERES PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: POT1PC, PARTIAL DNA BINDING DOMAIN, RESIDUES 198-339; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*GP*TP*TP*AP*CP*GP*GP*T)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: TELOMERIC SINGLE-STRANDED DNA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 3 ORGANISM_COMMON: FISSION YEAST; SOURCE 4 ORGANISM_TAXID: 284812; SOURCE 5 STRAIN: 972H-; SOURCE 6 GENE: POT1, SPAC26H5.06; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PTXB1; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 15 ORGANISM_TAXID: 284812 KEYWDS SPECIFICITY, PLASTICITY, PROMISCUITY, OB-FOLD, SSDNA BINDING, SINGLE- KEYWDS 2 STRANDED TELOMERIC DNA, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.H.DICKEY,D.S.WUTTKE REVDAT 3 15-NOV-17 4HIK 1 REMARK REVDAT 2 27-FEB-13 4HIK 1 JRNL REVDAT 1 12-DEC-12 4HIK 0 JRNL AUTH T.H.DICKEY,M.A.MCKERCHER,D.S.WUTTKE JRNL TITL NONSPECIFIC RECOGNITION IS ACHIEVED IN POT1PC THROUGH THE JRNL TITL 2 USE OF MULTIPLE BINDING MODES. JRNL REF STRUCTURE V. 21 121 2013 JRNL REFN ISSN 0969-2126 JRNL PMID 23201273 JRNL DOI 10.1016/J.STR.2012.10.015 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7_650 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 21007 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1051 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 35.3567 - 3.2706 0.99 2702 143 0.1847 0.1979 REMARK 3 2 3.2706 - 2.5963 1.00 2591 137 0.2071 0.2261 REMARK 3 3 2.5963 - 2.2681 1.00 2585 135 0.1986 0.2238 REMARK 3 4 2.2681 - 2.0608 0.99 2533 134 0.1875 0.2147 REMARK 3 5 2.0608 - 1.9131 0.98 2503 131 0.1752 0.1840 REMARK 3 6 1.9131 - 1.8003 0.98 2482 131 0.1852 0.2213 REMARK 3 7 1.8003 - 1.7101 0.95 2439 129 0.2070 0.2574 REMARK 3 8 1.7101 - 1.6357 0.84 2121 111 0.2376 0.2890 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 : 0.36 REMARK 3 B_SOL : 31.90 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.05680 REMARK 3 B22 (A**2) : -3.08540 REMARK 3 B33 (A**2) : -2.95140 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 : 0.006 1413 REMARK 3 ANGLE : 1.058 1949 REMARK 3 CHIRALITY : 0.075 202 REMARK 3 PLANARITY : 0.004 215 REMARK 3 DIHEDRAL : 15.952 536 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 4HIK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000075510. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 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) : 0.9799, 0.9801, 0.9428 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.636 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.13400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SNB REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% W/V PEG 4000, 0.2M AMMONIUM REMARK 280 FORMATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K 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 22.43500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.08500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.69500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.08500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.43500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.69500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL 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 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 MSE A 1 REMARK 465 SER A 2 REMARK 465 ASP A 3 REMARK 465 GLN A 142 REMARK 465 ASN A 143 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 338 O HOH A 340 2.01 REMARK 500 O HOH A 210 O HOH A 333 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 ASP A 73 -131.53 56.22 REMARK 500 TYR A 82 -56.05 -130.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HIO RELATED DB: PDB REMARK 900 THE SAME PROTEIN BOUND TO A DIFFERENT SSDNA SEQUENCE REMARK 900 RELATED ID: 4HIK RELATED DB: PDB REMARK 900 THE SAME PROTEIN BOUND TO A DIFFERENT SSDNA SEQUENCE REMARK 900 RELATED ID: 4HIM RELATED DB: PDB REMARK 900 THE SAME PROTEIN BOUND TO A DIFFERENT SSDNA SEQUENCE REMARK 900 RELATED ID: 4HJ5 RELATED DB: PDB REMARK 900 THE SAME PROTEIN BOUND TO A DIFFERENT SSDNA SEQUENCE REMARK 900 RELATED ID: 4HJ7 RELATED DB: PDB REMARK 900 THE SAME PROTEIN BOUND TO A DIFFERENT SSDNA SEQUENCE REMARK 900 RELATED ID: 4HJ8 RELATED DB: PDB REMARK 900 THE SAME PROTEIN BOUND TO A DIFFERENT SSDNA SEQUENCE REMARK 900 RELATED ID: 4HJ9 RELATED DB: PDB REMARK 900 THE SAME PROTEIN BOUND TO A DIFFERENT SSDNA SEQUENCE REMARK 900 RELATED ID: 4HJA RELATED DB: PDB REMARK 900 THE SAME PROTEIN BOUND TO A DIFFERENT SSDNA SEQUENCE DBREF 4HIK A 2 143 UNP O13988 POT1_SCHPO 198 339 DBREF 4HIK B 1 9 PDB 4HIK 4HIK 1 9 SEQADV 4HIK MSE A 1 UNP O13988 EXPRESSION TAG SEQADV 4HIK ASP A 3 UNP O13988 VAL 199 ENGINEERED MUTATION SEQRES 1 A 143 MSE SER ASP SER PHE SER LEU LEU SER GLN ILE THR PRO SEQRES 2 A 143 HIS GLN ARG CYS SER PHE TYR ALA GLN VAL ILE LYS THR SEQRES 3 A 143 TRP TYR SER ASP LYS ASN PHE THR LEU TYR VAL THR ASP SEQRES 4 A 143 TYR THR GLU ASN GLU LEU PHE PHE PRO MSE SER PRO TYR SEQRES 5 A 143 THR SER SER SER ARG TRP ARG GLY PRO PHE GLY ARG PHE SEQRES 6 A 143 SER ILE ARG CYS ILE LEU TRP ASP GLU HIS ASP PHE TYR SEQRES 7 A 143 CYS ARG ASN TYR ILE LYS GLU GLY ASP TYR VAL VAL MSE SEQRES 8 A 143 LYS ASN VAL ARG THR LYS ILE ASP HIS LEU GLY TYR LEU SEQRES 9 A 143 GLU CYS ILE LEU HIS GLY ASP SER ALA LYS ARG TYR ASN SEQRES 10 A 143 MSE SER ILE GLU LYS VAL ASP SER GLU GLU PRO GLU LEU SEQRES 11 A 143 ASN GLU ILE LYS SER ARG LYS ARG LEU TYR VAL GLN ASN SEQRES 1 B 9 DG DG DT DT DA DC DG DG DT MODRES 4HIK MSE A 49 MET SELENOMETHIONINE MODRES 4HIK MSE A 91 MET SELENOMETHIONINE MODRES 4HIK MSE A 118 MET SELENOMETHIONINE HET MSE A 49 8 HET MSE A 91 8 HET MSE A 118 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 3 HOH *175(H2 O) HELIX 1 1 LEU A 7 ILE A 11 5 5 HELIX 2 2 TRP A 72 ARG A 80 1 9 HELIX 3 3 GLU A 127 GLU A 129 5 3 HELIX 4 4 LEU A 130 ARG A 138 1 9 HELIX 5 5 LEU A 139 VAL A 141 5 3 SHEET 1 A 7 SER A 119 VAL A 123 0 SHEET 2 A 7 TYR A 88 ILE A 98 -1 N LYS A 92 O SER A 119 SHEET 3 A 7 LEU A 104 LEU A 108 -1 O ILE A 107 N ARG A 95 SHEET 4 A 7 ILE A 67 LEU A 71 1 N ILE A 70 O CYS A 106 SHEET 5 A 7 PHE A 33 THR A 38 -1 N LEU A 35 O CYS A 69 SHEET 6 A 7 ARG A 16 TYR A 28 -1 N ILE A 24 O TYR A 36 SHEET 7 A 7 TYR A 88 ILE A 98 -1 O VAL A 89 N ALA A 21 LINK C PRO A 48 N MSE A 49 1555 1555 1.33 LINK C MSE A 49 N SER A 50 1555 1555 1.33 LINK C VAL A 90 N MSE A 91 1555 1555 1.33 LINK C MSE A 91 N LYS A 92 1555 1555 1.33 LINK C ASN A 117 N MSE A 118 1555 1555 1.33 LINK C MSE A 118 N SER A 119 1555 1555 1.32 CISPEP 1 GLY A 60 PRO A 61 0 -0.75 CRYST1 44.870 57.390 66.170 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 0.022287 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017425 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015113 0.00000