HEADER CELL CYCLE 29-SEP-17 6B5C TITLE STRUCTURAL BASIS FOR KATANIN SELF-ASSEMBLY COMPND MOL_ID: 1; COMPND 2 MOLECULE: KATANIN P60 ATPASE-CONTAINING SUBUNIT A-LIKE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: KATANIN P60 SUBUNIT A-LIKE 1,P60 KATANIN-LIKE 1; COMPND 5 EC: 3.6.4.3; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KATNAL1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS KATANIN, AAA ATPASE, MICROTUBULE SEVERING PROTEIN, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR S.NITHIANANTHAM,J.AL-BASSAM REVDAT 4 04-OCT-23 6B5C 1 REMARK REVDAT 3 01-JAN-20 6B5C 1 REMARK REVDAT 2 18-JUL-18 6B5C 1 SOURCE JRNL REVDAT 1 23-MAY-18 6B5C 0 JRNL AUTH S.NITHIANANTHAM,F.J.MCNALLY,J.AL-BASSAM JRNL TITL STRUCTURAL BASIS FOR DISASSEMBLY OF KATANIN JRNL TITL 2 HETERODODECAMERS. JRNL REF J. BIOL. CHEM. V. 293 10590 2018 JRNL REFN ESSN 1083-351X JRNL PMID 29752405 JRNL DOI 10.1074/JBC.RA117.001215 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 11888 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.220 REMARK 3 FREE R VALUE TEST SET COUNT : 620 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 58.8276 - 3.8096 1.00 2944 162 0.1931 0.2164 REMARK 3 2 3.8096 - 3.0238 1.00 2811 150 0.2125 0.2468 REMARK 3 3 3.0238 - 2.6416 1.00 2751 158 0.2590 0.3329 REMARK 3 4 2.6416 - 2.4000 1.00 2762 150 0.2639 0.3255 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.74 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.33 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 : 0.002 2368 REMARK 3 ANGLE : 0.502 3183 REMARK 3 CHIRALITY : 0.038 361 REMARK 3 PLANARITY : 0.003 403 REMARK 3 DIHEDRAL : 14.827 1478 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 13.4383 35.4470 73.3184 REMARK 3 T TENSOR REMARK 3 T11: 0.2066 T22: 0.3052 REMARK 3 T33: 0.2550 T12: 0.0069 REMARK 3 T13: 0.0338 T23: -0.0147 REMARK 3 L TENSOR REMARK 3 L11: 0.2762 L22: 2.3830 REMARK 3 L33: 0.5617 L12: 0.1705 REMARK 3 L13: 0.2380 L23: -0.3234 REMARK 3 S TENSOR REMARK 3 S11: 0.0132 S12: -0.0640 S13: -0.0148 REMARK 3 S21: 0.0709 S22: -0.0335 S23: 0.0051 REMARK 3 S31: 0.0700 S32: 0.0099 S33: 0.0157 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 6B5C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1000230303. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : CRYO-COOLED DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11932 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 58.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09400 REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.56900 REMARK 200 R SYM FOR SHELL (I) : 0.56900 REMARK 200 FOR SHELL : 1.400 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: 6B5D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH 8.0 AND 18% PEG 8000, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 20.05000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.81000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.59500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.81000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.05000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.59500 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 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 TYR A 281 REMARK 465 ARG A 282 REMARK 465 GLY A 283 REMARK 465 GLU A 284 REMARK 465 ARG A 316 REMARK 465 GLY A 317 REMARK 465 GLY A 340 REMARK 465 GLY A 341 REMARK 465 ALA A 342 REMARK 465 LEU A 343 REMARK 465 GLU A 344 REMARK 465 ASN A 345 REMARK 465 ASP A 346 REMARK 465 ASP A 347 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 212 -139.18 58.48 REMARK 500 ALA A 300 -66.18 -11.69 REMARK 500 LYS A 350 63.58 -100.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 501 DBREF 6B5C A 184 490 UNP Q9BW62 KATL1_HUMAN 184 490 SEQADV 6B5C GLN A 308 UNP Q9BW62 GLU 308 ENGINEERED MUTATION SEQRES 1 A 307 ALA GLY TYR ASP LYS ASP LEU VAL GLU ALA LEU GLU ARG SEQRES 2 A 307 ASP ILE VAL SER ARG ASN PRO SER ILE HIS TRP ASP ASP SEQRES 3 A 307 ILE ALA ASP LEU GLU GLU ALA LYS LYS LEU LEU ARG GLU SEQRES 4 A 307 ALA VAL VAL LEU PRO MET TRP MET PRO ASP PHE PHE LYS SEQRES 5 A 307 GLY ILE ARG ARG PRO TRP LYS GLY VAL LEU MET VAL GLY SEQRES 6 A 307 PRO PRO GLY THR GLY LYS THR MET LEU ALA LYS ALA VAL SEQRES 7 A 307 ALA THR GLU CYS GLY THR THR PHE PHE ASN VAL SER SER SEQRES 8 A 307 SER THR LEU THR SER LYS TYR ARG GLY GLU SER GLU LYS SEQRES 9 A 307 LEU VAL ARG LEU LEU PHE GLU MET ALA ARG PHE TYR ALA SEQRES 10 A 307 PRO THR THR ILE PHE ILE ASP GLN ILE ASP SER ILE CYS SEQRES 11 A 307 SER ARG ARG GLY THR SER ASP GLU HIS GLU ALA SER ARG SEQRES 12 A 307 ARG VAL LYS SER GLU LEU LEU ILE GLN MET ASP GLY VAL SEQRES 13 A 307 GLY GLY ALA LEU GLU ASN ASP ASP PRO SER LYS MET VAL SEQRES 14 A 307 MET VAL LEU ALA ALA THR ASN PHE PRO TRP ASP ILE ASP SEQRES 15 A 307 GLU ALA LEU ARG ARG ARG LEU GLU LYS ARG ILE TYR ILE SEQRES 16 A 307 PRO LEU PRO THR ALA LYS GLY ARG ALA GLU LEU LEU LYS SEQRES 17 A 307 ILE ASN LEU ARG GLU VAL GLU LEU ASP PRO ASP ILE GLN SEQRES 18 A 307 LEU GLU ASP ILE ALA GLU LYS ILE GLU GLY TYR SER GLY SEQRES 19 A 307 ALA ASP ILE THR ASN VAL CYS ARG ASP ALA SER LEU MET SEQRES 20 A 307 ALA MET ARG ARG ARG ILE ASN GLY LEU SER PRO GLU GLU SEQRES 21 A 307 ILE ARG ALA LEU SER LYS GLU GLU LEU GLN MET PRO VAL SEQRES 22 A 307 THR LYS GLY ASP PHE GLU LEU ALA LEU LYS LYS ILE ALA SEQRES 23 A 307 LYS SER VAL SER ALA ALA ASP LEU GLU LYS TYR GLU LYS SEQRES 24 A 307 TRP MET VAL GLU PHE GLY SER ALA HET PG4 A 501 13 HETNAM PG4 TETRAETHYLENE GLYCOL FORMUL 2 PG4 C8 H18 O5 FORMUL 3 HOH *53(H2 O) HELIX 1 AA1 GLY A 185 VAL A 199 1 15 HELIX 2 AA2 HIS A 206 ILE A 210 5 5 HELIX 3 AA3 LEU A 213 VAL A 225 1 13 HELIX 4 AA4 VAL A 225 MET A 230 1 6 HELIX 5 AA5 MET A 230 ILE A 237 1 8 HELIX 6 AA6 GLY A 253 GLY A 266 1 14 HELIX 7 AA7 SER A 274 LYS A 280 1 7 HELIX 8 AA8 GLU A 286 TYR A 299 1 14 HELIX 9 AA9 GLN A 308 SER A 314 5 7 HELIX 10 AB1 SER A 319 VAL A 339 1 21 HELIX 11 AB2 PHE A 360 ILE A 364 5 5 HELIX 12 AB3 ASP A 365 ARG A 370 1 6 HELIX 13 AB4 THR A 382 LEU A 394 1 13 HELIX 14 AB5 GLN A 404 ILE A 412 1 9 HELIX 15 AB6 SER A 416 LEU A 439 1 24 HELIX 16 AB7 SER A 440 LEU A 447 1 8 HELIX 17 AB8 SER A 448 GLN A 453 1 6 HELIX 18 AB9 THR A 457 ILE A 468 1 12 HELIX 19 AC1 SER A 473 GLY A 488 1 16 SHEET 1 AA1 5 THR A 268 SER A 273 0 SHEET 2 AA1 5 THR A 302 ASP A 307 1 O THR A 303 N THR A 268 SHEET 3 AA1 5 VAL A 352 THR A 358 1 O LEU A 355 N ILE A 304 SHEET 4 AA1 5 VAL A 244 VAL A 247 1 N MET A 246 O ALA A 356 SHEET 5 AA1 5 LYS A 374 TYR A 377 1 O LYS A 374 N LEU A 245 SITE 1 AC1 8 HIS A 206 GLU A 222 ARG A 238 ARG A 239 SITE 2 AC1 8 TRP A 241 GLU A 478 GLU A 481 HOH A 636 CRYST1 40.100 61.190 117.620 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 0.024938 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016343 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008502 0.00000