HEADER TRANSFERASE 28-FEB-24 8YHK TITLE THE CRYSTAL STRUCTURE OF P21-ACTIVATED KINASES PAK4 FROM BIORTUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE PAK 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: P21-ACTIVATED KINASE 4,PAK-4; COMPND 5 EC: 2.7.11.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PAK4, KIAA1142; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS KINASE, SERINE/THREONINE-PROTEIN KINASE, APOPTOSIS, ATP-BINDING, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR F.WANG,W.CHENG,Z.LV,J.QI,B.WU REVDAT 1 13-MAR-24 8YHK 0 JRNL AUTH F.WANG,W.CHENG,Z.LV,J.QI,B.WU JRNL TITL THE CRYSTAL STRUCTURE OF P21-ACTIVATED KINASES PAK4 FROM JRNL TITL 2 BIORTUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 7154 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.249 REMARK 3 FREE R VALUE : 0.319 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.906 REMARK 3 FREE R VALUE TEST SET COUNT : 351 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 46.2990 - 14.6190 0.90 97 5 0.3400 0.6100 REMARK 3 2 14.6190 - 10.3890 0.88 151 10 0.1500 0.2070 REMARK 3 3 10.3890 - 8.4970 0.95 195 8 0.1450 0.1500 REMARK 3 4 8.4970 - 7.3650 0.95 231 8 0.1280 0.1540 REMARK 3 5 7.3650 - 6.5910 0.90 250 7 0.1380 0.2120 REMARK 3 6 6.5910 - 6.0180 0.93 277 14 0.1820 0.2010 REMARK 3 7 6.0180 - 5.5730 0.96 291 18 0.2350 0.4140 REMARK 3 8 5.5730 - 5.2140 0.90 312 10 0.2500 0.3310 REMARK 3 9 5.2140 - 4.9170 0.93 313 18 0.2320 0.3040 REMARK 3 10 4.9170 - 4.6650 0.91 353 22 0.2070 0.3130 REMARK 3 11 4.6650 - 4.4480 0.98 375 16 0.2140 0.2460 REMARK 3 12 4.4480 - 4.2590 0.93 377 23 0.2100 0.3100 REMARK 3 13 4.2590 - 4.0920 0.95 393 28 0.2360 0.4140 REMARK 3 14 4.0920 - 3.9440 0.98 414 25 0.2820 0.2420 REMARK 3 15 3.9440 - 3.8100 0.92 419 23 0.3050 0.4340 REMARK 3 16 3.8100 - 3.6890 0.99 461 21 0.3540 0.3270 REMARK 3 17 3.6890 - 3.5790 0.94 455 21 0.3860 0.3540 REMARK 3 18 3.5790 - 3.4790 0.94 463 22 0.3830 0.4250 REMARK 3 19 3.4790 - 3.3860 1.00 491 24 0.4610 0.5140 REMARK 3 20 3.3860 - 3.3000 0.94 485 28 0.4460 0.4530 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.602 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 102.9 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.99200 REMARK 3 B22 (A**2) : -8.99200 REMARK 3 B33 (A**2) : 17.98300 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 : 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: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8YHK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 01-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1300045676. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-23 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 : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95373 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7176 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 REMARK 200 RESOLUTION RANGE LOW (A) : 48.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.56 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4 M POTASSIUM SODIUM TARTRATE REMARK 280 TETRAHYDRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 21.84000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 73.13700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 73.13700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.76000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 73.13700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 73.13700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 10.92000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 73.13700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 73.13700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.76000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 73.13700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 73.13700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 10.92000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 21.84000 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 TOTAL BURIED SURFACE AREA: 70 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 SER A 291 REMARK 465 PRO A 292 REMARK 465 GLN A 293 REMARK 465 ARG A 294 REMARK 465 GLU A 295 REMARK 465 PRO A 296 REMARK 465 GLN A 297 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 322 -54.63 -131.99 REMARK 500 CYS A 336 127.34 -39.00 REMARK 500 VAL A 367 -49.87 88.14 REMARK 500 ASP A 372 -26.21 73.28 REMARK 500 PHE A 461 47.93 -109.96 REMARK 500 SER A 474 128.17 -27.71 REMARK 500 ASN A 537 54.66 -92.25 REMARK 500 ALA A 575 113.92 -38.76 REMARK 500 REMARK 500 REMARK: NULL DBREF 8YHK A 291 591 UNP O96013 PAK4_HUMAN 291 591 SEQRES 1 A 301 SER PRO GLN ARG GLU PRO GLN ARG VAL SER HIS GLU GLN SEQRES 2 A 301 PHE ARG ALA ALA LEU GLN LEU VAL VAL ASP PRO GLY ASP SEQRES 3 A 301 PRO ARG SER TYR LEU ASP ASN PHE ILE LYS ILE GLY GLU SEQRES 4 A 301 GLY SER THR GLY ILE VAL CYS ILE ALA THR VAL ARG SER SEQRES 5 A 301 SER GLY LYS LEU VAL ALA VAL LYS LYS MET ASP LEU ARG SEQRES 6 A 301 LYS GLN GLN ARG ARG GLU LEU LEU PHE ASN GLU VAL VAL SEQRES 7 A 301 ILE MET ARG ASP TYR GLN HIS GLU ASN VAL VAL GLU MET SEQRES 8 A 301 TYR ASN SER TYR LEU VAL GLY ASP GLU LEU TRP VAL VAL SEQRES 9 A 301 MET GLU PHE LEU GLU GLY GLY ALA LEU THR ASP ILE VAL SEQRES 10 A 301 THR HIS THR ARG MET ASN GLU GLU GLN ILE ALA ALA VAL SEQRES 11 A 301 CYS LEU ALA VAL LEU GLN ALA LEU SER VAL LEU HIS ALA SEQRES 12 A 301 GLN GLY VAL ILE HIS ARG ASP ILE LYS SER ASP SER ILE SEQRES 13 A 301 LEU LEU THR HIS ASP GLY ARG VAL LYS LEU SER ASP PHE SEQRES 14 A 301 GLY PHE CYS ALA GLN VAL SER LYS GLU VAL PRO ARG ARG SEQRES 15 A 301 LYS SER LEU VAL GLY THR PRO TYR TRP MET ALA PRO GLU SEQRES 16 A 301 LEU ILE SER ARG LEU PRO TYR GLY PRO GLU VAL ASP ILE SEQRES 17 A 301 TRP SER LEU GLY ILE MET VAL ILE GLU MET VAL ASP GLY SEQRES 18 A 301 GLU PRO PRO TYR PHE ASN GLU PRO PRO LEU LYS ALA MET SEQRES 19 A 301 LYS MET ILE ARG ASP ASN LEU PRO PRO ARG LEU LYS ASN SEQRES 20 A 301 LEU HIS LYS VAL SER PRO SER LEU LYS GLY PHE LEU ASP SEQRES 21 A 301 ARG LEU LEU VAL ARG ASP PRO ALA GLN ARG ALA THR ALA SEQRES 22 A 301 ALA GLU LEU LEU LYS HIS PRO PHE LEU ALA LYS ALA GLY SEQRES 23 A 301 PRO PRO ALA SER ILE VAL PRO LEU MET ARG GLN ASN ARG SEQRES 24 A 301 THR ARG HET PGE A 601 10 HETNAM PGE TRIETHYLENE GLYCOL FORMUL 2 PGE C6 H14 O4 FORMUL 3 HOH *11(H2 O) HELIX 1 AA1 SER A 300 VAL A 312 1 13 HELIX 2 AA2 ASP A 316 TYR A 320 5 5 HELIX 3 AA3 ARG A 359 LEU A 363 5 5 HELIX 4 AA4 PHE A 364 ILE A 369 1 6 HELIX 5 AA5 LEU A 403 THR A 410 1 8 HELIX 6 AA6 ASN A 413 GLY A 435 1 23 HELIX 7 AA7 LYS A 442 ASP A 444 5 3 HELIX 8 AA8 ASP A 458 GLY A 460 5 3 HELIX 9 AA9 THR A 478 MET A 482 5 5 HELIX 10 AB1 ALA A 483 SER A 488 1 6 HELIX 11 AB2 GLU A 495 GLY A 511 1 17 HELIX 12 AB3 PRO A 519 ASN A 530 1 12 HELIX 13 AB4 SER A 542 LEU A 553 1 12 HELIX 14 AB5 THR A 562 LYS A 568 1 7 HELIX 15 AB6 HIS A 569 LYS A 574 5 6 HELIX 16 AB7 PRO A 577 ARG A 589 5 13 SHEET 1 AA1 4 ILE A 337 THR A 339 0 SHEET 2 AA1 4 LEU A 346 ASP A 353 -1 O VAL A 347 N ALA A 338 SHEET 3 AA1 4 GLU A 390 GLU A 396 -1 O MET A 395 N ALA A 348 SHEET 4 AA1 4 MET A 381 VAL A 387 -1 N VAL A 387 O GLU A 390 SHEET 1 AA2 3 GLY A 401 ALA A 402 0 SHEET 2 AA2 3 ILE A 446 LEU A 448 -1 O LEU A 448 N GLY A 401 SHEET 3 AA2 3 VAL A 454 LEU A 456 -1 O LYS A 455 N LEU A 447 SHEET 1 AA3 2 VAL A 436 HIS A 438 0 SHEET 2 AA3 2 CYS A 462 GLN A 464 -1 O ALA A 463 N ILE A 437 CRYST1 146.274 146.274 43.680 90.00 90.00 90.00 P 43 21 2 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 0.006836 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006836 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022894 0.00000