HEADER RNA BINDING PROTEIN 24-SEP-21 7SBE TITLE STRUCTURE OF THE K. LACTIS TELOMERASE RNA BINDING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TELOMERASE REVERSE TRANSCRIPTASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RNA BINDING DOMAIN; COMPND 5 SYNONYM: TELOMERASE CATALYTIC SUBUNIT; COMPND 6 EC: 2.7.7.49; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLUYVEROMYCES LACTIS; SOURCE 3 ORGANISM_COMMON: YEAST, CANDIDA SPHAERICA; SOURCE 4 ORGANISM_TAXID: 28985; SOURCE 5 GENE: KLLA0_C18381G; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA PHAGE ECSZW-2; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 2419741 KEYWDS TELOMERASE, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.SKORDALAKES,Y.TZFATI REVDAT 2 18-OCT-23 7SBE 1 REMARK REVDAT 1 21-SEP-22 7SBE 0 JRNL AUTH E.SKORDALAKES,Y.TZFATI JRNL TITL STRUCTURE OF THE K. LACTIS TELOMERASE RNA BINDING DOMAIN JRNL REF INT J MOL SCI 2022 JRNL REFN ESSN 1422-0067 REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 15832 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 790 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 19.7100 - 4.8000 0.99 2547 135 0.2004 0.2427 REMARK 3 2 4.8000 - 3.8200 1.00 2523 133 0.2003 0.2649 REMARK 3 3 3.8200 - 3.3400 1.00 2524 132 0.2573 0.3042 REMARK 3 4 3.3400 - 3.0300 1.00 2474 129 0.2990 0.3624 REMARK 3 5 3.0300 - 2.8200 0.99 2494 130 0.3312 0.3649 REMARK 3 6 2.8200 - 2.6500 0.99 2480 131 0.4361 0.5077 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) : 0.470 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 38.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 91.44 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7SBE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1000259969. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15880 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.72 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: PHENIX REMARK 200 STARTING MODEL: 2R4G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% PEG3350 AND 200 MM NA.CITRATE, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 70.18500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 70.18500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 42.50000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 SER A 168 REMARK 465 ASN A 169 REMARK 465 ILE A 170 REMARK 465 GLU A 171 REMARK 465 ARG A 172 REMARK 465 ASN A 173 REMARK 465 THR A 174 REMARK 465 LYS A 175 REMARK 465 ARG A 404 REMARK 465 SER B 168 REMARK 465 ASN B 169 REMARK 465 ILE B 170 REMARK 465 GLU B 171 REMARK 465 ARG B 172 REMARK 465 ASN B 173 REMARK 465 THR B 174 REMARK 465 LYS B 175 REMARK 465 ARG B 404 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 GLN A 191 14.73 57.20 REMARK 500 GLU A 198 108.82 -57.51 REMARK 500 SER A 256 -168.75 -127.34 REMARK 500 SER A 377 -7.89 77.54 REMARK 500 SER A 378 -148.06 -113.45 REMARK 500 TYR A 401 3.14 -150.25 REMARK 500 HIS B 186 -74.20 -78.06 REMARK 500 GLU B 198 106.22 -56.95 REMARK 500 LYS B 211 -21.26 73.44 REMARK 500 LYS B 255 86.43 -59.30 REMARK 500 HIS B 305 72.10 53.57 REMARK 500 GLU B 334 94.58 -60.37 REMARK 500 VAL B 344 -18.44 -48.77 REMARK 500 SER B 378 -130.67 61.49 REMARK 500 REMARK 500 REMARK: NULL DBREF 7SBE A 171 404 UNP Q6CSS0 Q6CSS0_KLULA 171 404 DBREF 7SBE B 171 404 UNP Q6CSS0 Q6CSS0_KLULA 171 404 SEQADV 7SBE SER A 168 UNP Q6CSS0 EXPRESSION TAG SEQADV 7SBE ASN A 169 UNP Q6CSS0 EXPRESSION TAG SEQADV 7SBE ILE A 170 UNP Q6CSS0 EXPRESSION TAG SEQADV 7SBE SER B 168 UNP Q6CSS0 EXPRESSION TAG SEQADV 7SBE ASN B 169 UNP Q6CSS0 EXPRESSION TAG SEQADV 7SBE ILE B 170 UNP Q6CSS0 EXPRESSION TAG SEQRES 1 A 237 SER ASN ILE GLU ARG ASN THR LYS LEU THR ILE ASP TRP SEQRES 2 A 237 ASN SER ALA LEU TYR HIS LYS ILE ARG PRO GLN ASP TYR SEQRES 3 A 237 LYS ASN ILE ILE GLU THR ASP GLN GLY LEU LEU ILE ALA SEQRES 4 A 237 GLU ILE PHE PRO LYS ILE SER GLU SER SER LYS THR PRO SEQRES 5 A 237 ARG SER LEU ASN PHE ALA LEU ASN ASN LEU LYS PRO ILE SEQRES 6 A 237 LEU TYR GLU LEU ILE ARG ALA HIS GLU ARG PHE SER TYR SEQRES 7 A 237 ARG HIS ILE ILE ASN ASN ILE CYS PRO LYS SER ASP THR SEQRES 8 A 237 PHE TYR SER SER PRO LYS SER VAL ILE LYS LEU LEU ILE SEQRES 9 A 237 VAL CYS VAL ARG LYS THR PHE PRO LEU ASP LEU LEU GLY SEQRES 10 A 237 SER ASN SER ASN TYR SER VAL LEU SER LYS ALA ILE ALA SEQRES 11 A 237 ILE LEU VAL LYS LYS PRO LEU HIS SER LYS ILE LEU PHE SEQRES 12 A 237 ASP GLU LEU CYS LYS GLY LEU ARG VAL LYS ASP VAL LYS SEQRES 13 A 237 TRP LEU GLU THR ARG ARG LEU PRO ALA GLY GLU GLN THR SEQRES 14 A 237 GLN LYS ILE PRO TYR TYR ASP VAL LYS ASN ARG GLN ALA SEQRES 15 A 237 LEU LEU TYR LYS LEU PHE PHE TRP ILE LEU SER CYS TYR SEQRES 16 A 237 VAL PRO LYS LEU LEU SER THR PHE PHE TYR VAL THR GLU SEQRES 17 A 237 LEU SER SER THR VAL ASP ILE VAL TYR ILE ARG HIS ASP SEQRES 18 A 237 THR TRP LYS THR MET SER GLN PRO PHE LEU LYS SER TYR SEQRES 19 A 237 PHE ARG ARG SEQRES 1 B 237 SER ASN ILE GLU ARG ASN THR LYS LEU THR ILE ASP TRP SEQRES 2 B 237 ASN SER ALA LEU TYR HIS LYS ILE ARG PRO GLN ASP TYR SEQRES 3 B 237 LYS ASN ILE ILE GLU THR ASP GLN GLY LEU LEU ILE ALA SEQRES 4 B 237 GLU ILE PHE PRO LYS ILE SER GLU SER SER LYS THR PRO SEQRES 5 B 237 ARG SER LEU ASN PHE ALA LEU ASN ASN LEU LYS PRO ILE SEQRES 6 B 237 LEU TYR GLU LEU ILE ARG ALA HIS GLU ARG PHE SER TYR SEQRES 7 B 237 ARG HIS ILE ILE ASN ASN ILE CYS PRO LYS SER ASP THR SEQRES 8 B 237 PHE TYR SER SER PRO LYS SER VAL ILE LYS LEU LEU ILE SEQRES 9 B 237 VAL CYS VAL ARG LYS THR PHE PRO LEU ASP LEU LEU GLY SEQRES 10 B 237 SER ASN SER ASN TYR SER VAL LEU SER LYS ALA ILE ALA SEQRES 11 B 237 ILE LEU VAL LYS LYS PRO LEU HIS SER LYS ILE LEU PHE SEQRES 12 B 237 ASP GLU LEU CYS LYS GLY LEU ARG VAL LYS ASP VAL LYS SEQRES 13 B 237 TRP LEU GLU THR ARG ARG LEU PRO ALA GLY GLU GLN THR SEQRES 14 B 237 GLN LYS ILE PRO TYR TYR ASP VAL LYS ASN ARG GLN ALA SEQRES 15 B 237 LEU LEU TYR LYS LEU PHE PHE TRP ILE LEU SER CYS TYR SEQRES 16 B 237 VAL PRO LYS LEU LEU SER THR PHE PHE TYR VAL THR GLU SEQRES 17 B 237 LEU SER SER THR VAL ASP ILE VAL TYR ILE ARG HIS ASP SEQRES 18 B 237 THR TRP LYS THR MET SER GLN PRO PHE LEU LYS SER TYR SEQRES 19 B 237 PHE ARG ARG FORMUL 3 HOH *4(H2 O) HELIX 1 AA1 ASP A 179 TYR A 185 1 7 HELIX 2 AA2 ASP A 192 ILE A 197 5 6 HELIX 3 AA3 ASP A 200 PHE A 209 1 10 HELIX 4 AA4 PRO A 219 ARG A 242 1 24 HELIX 5 AA5 SER A 244 CYS A 253 1 10 HELIX 6 AA6 SER A 262 PHE A 278 1 17 HELIX 7 AA7 SER A 285 LYS A 302 1 18 HELIX 8 AA8 VAL A 322 GLU A 326 5 5 HELIX 9 AA9 PRO A 340 CYS A 361 1 22 HELIX 10 AB1 CYS A 361 PHE A 370 1 10 HELIX 11 AB2 HIS A 387 SER A 400 1 14 HELIX 12 AB3 TRP B 180 TYR B 185 1 6 HELIX 13 AB4 ASP B 192 ILE B 196 5 5 HELIX 14 AB5 ASP B 200 PHE B 209 1 10 HELIX 15 AB6 PRO B 219 ARG B 242 1 24 HELIX 16 AB7 SER B 244 CYS B 253 1 10 HELIX 17 AB8 SER B 262 PHE B 278 1 17 HELIX 18 AB9 SER B 285 LYS B 301 1 17 HELIX 19 AC1 PHE B 310 CYS B 314 1 5 HELIX 20 AC2 ARG B 318 GLU B 326 5 9 HELIX 21 AC3 PRO B 340 CYS B 361 1 22 HELIX 22 AC4 CYS B 361 PHE B 370 1 10 HELIX 23 AC5 HIS B 387 SER B 400 1 14 SHEET 1 AA1 2 PHE A 371 THR A 374 0 SHEET 2 AA1 2 VAL A 383 ARG A 386 -1 O VAL A 383 N THR A 374 SHEET 1 AA2 2 THR B 177 ASP B 179 0 SHEET 2 AA2 2 LYS B 307 LEU B 309 -1 O ILE B 308 N ILE B 178 SHEET 1 AA3 2 PHE B 371 THR B 374 0 SHEET 2 AA3 2 VAL B 383 ARG B 386 -1 O ILE B 385 N TYR B 372 CRYST1 140.370 85.000 48.420 90.00 106.11 90.00 C 1 2 1 8 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 0.007124 0.000000 0.002057 0.00000 SCALE2 0.000000 0.011765 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021497 0.00000