HEADER TRANSFERASE 02-OCT-19 6L24 TITLE CRYSTAL STRUCTURE OF CK2A1 H115Y/V116I WITH HEMATEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CASEIN KINASE II SUBUNIT ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CK II ALPHA; COMPND 5 EC: 2.7.11.1; 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: CSNK2A1, CK2A1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN KINASE, TRANSFERASE, INHIBITOR, COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.TSUYUGUCHI,T.KINOSHITA REVDAT 2 22-NOV-23 6L24 1 REMARK REVDAT 1 26-FEB-20 6L24 0 JRNL AUTH M.TSUYUGUCHI,T.NAKANIWA,A.HIRASAWA,I.NAKANISHI,T.KINOSHITA JRNL TITL STRUCTURAL INSIGHTS FOR PRODUCING CK2 ALPHA 1-SPECIFIC JRNL TITL 2 INHIBITORS. JRNL REF BIOORG.MED.CHEM.LETT. V. 30 26837 2020 JRNL REFN ESSN 1464-3405 JRNL PMID 31859160 JRNL DOI 10.1016/J.BMCL.2019.126837 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692+SVN 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.338 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 13277 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.032 REMARK 3 FREE R VALUE TEST SET COUNT : 1332 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 43.3400 - 5.1682 1.00 1286 143 0.1919 0.2436 REMARK 3 2 5.1682 - 4.1032 1.00 1214 138 0.1545 0.2129 REMARK 3 3 4.1032 - 3.5848 1.00 1214 135 0.1701 0.2447 REMARK 3 4 3.5848 - 3.2572 1.00 1178 130 0.1786 0.2765 REMARK 3 5 3.2572 - 3.0238 1.00 1185 131 0.1950 0.2855 REMARK 3 6 3.0238 - 2.8455 1.00 1187 132 0.1935 0.3029 REMARK 3 7 2.8455 - 2.7030 1.00 1169 129 0.1840 0.2544 REMARK 3 8 2.7030 - 2.5854 1.00 1169 133 0.2097 0.3300 REMARK 3 9 2.5854 - 2.4859 1.00 1171 133 0.2017 0.2730 REMARK 3 10 2.4859 - 2.4001 1.00 1172 128 0.2296 0.3710 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.311 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.52 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 2945 REMARK 3 ANGLE : 1.242 3994 REMARK 3 CHIRALITY : 0.045 407 REMARK 3 PLANARITY : 0.005 507 REMARK 3 DIHEDRAL : 16.670 1106 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 6L24 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1300013649. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13323 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 43.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.19300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0000 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) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.84500 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: 3WAR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ETHYLENE GLYCOL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 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 25.79400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.98200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.41150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.98200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.79400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.41150 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 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 GLY A -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 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 NZ LYS A 68 O18 E3U A 401 2.19 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 ARG A 21 170.99 -49.67 REMARK 500 GLU A 22 -18.34 73.32 REMARK 500 ASN A 61 12.63 -150.48 REMARK 500 ASN A 117 80.49 -69.28 REMARK 500 TYR A 125 -5.01 149.52 REMARK 500 ASP A 156 36.56 -151.40 REMARK 500 ASP A 175 84.81 52.33 REMARK 500 ALA A 193 157.38 62.04 REMARK 500 MET A 208 54.82 -98.52 REMARK 500 GLU A 264 109.50 68.06 REMARK 500 ASP A 266 144.82 -25.66 REMARK 500 PRO A 267 -80.87 -34.03 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 E3U A 401 DBREF 6L24 A 1 335 UNP P68400 CSK21_HUMAN 1 335 SEQADV 6L24 GLY A -4 UNP P68400 EXPRESSION TAG SEQADV 6L24 PRO A -3 UNP P68400 EXPRESSION TAG SEQADV 6L24 LEU A -2 UNP P68400 EXPRESSION TAG SEQADV 6L24 GLY A -1 UNP P68400 EXPRESSION TAG SEQADV 6L24 SER A 0 UNP P68400 EXPRESSION TAG SEQADV 6L24 TYR A 115 UNP P68400 HIS 115 ENGINEERED MUTATION SEQADV 6L24 ILE A 116 UNP P68400 VAL 116 ENGINEERED MUTATION SEQRES 1 A 340 GLY PRO LEU GLY SER MET SER GLY PRO VAL PRO SER ARG SEQRES 2 A 340 ALA ARG VAL TYR THR ASP VAL ASN THR HIS ARG PRO ARG SEQRES 3 A 340 GLU TYR TRP ASP TYR GLU SER HIS VAL VAL GLU TRP GLY SEQRES 4 A 340 ASN GLN ASP ASP TYR GLN LEU VAL ARG LYS LEU GLY ARG SEQRES 5 A 340 GLY LYS TYR SER GLU VAL PHE GLU ALA ILE ASN ILE THR SEQRES 6 A 340 ASN ASN GLU LYS VAL VAL VAL LYS ILE LEU LYS PRO VAL SEQRES 7 A 340 LYS LYS LYS LYS ILE LYS ARG GLU ILE LYS ILE LEU GLU SEQRES 8 A 340 ASN LEU ARG GLY GLY PRO ASN ILE ILE THR LEU ALA ASP SEQRES 9 A 340 ILE VAL LYS ASP PRO VAL SER ARG THR PRO ALA LEU VAL SEQRES 10 A 340 PHE GLU TYR ILE ASN ASN THR ASP PHE LYS GLN LEU TYR SEQRES 11 A 340 GLN THR LEU THR ASP TYR ASP ILE ARG PHE TYR MET TYR SEQRES 12 A 340 GLU ILE LEU LYS ALA LEU ASP TYR CYS HIS SER MET GLY SEQRES 13 A 340 ILE MET HIS ARG ASP VAL LYS PRO HIS ASN VAL MET ILE SEQRES 14 A 340 ASP HIS GLU HIS ARG LYS LEU ARG LEU ILE ASP TRP GLY SEQRES 15 A 340 LEU ALA GLU PHE TYR HIS PRO GLY GLN GLU TYR ASN VAL SEQRES 16 A 340 ARG VAL ALA SER ARG TYR PHE LYS GLY PRO GLU LEU LEU SEQRES 17 A 340 VAL ASP TYR GLN MET TYR ASP TYR SER LEU ASP MET TRP SEQRES 18 A 340 SER LEU GLY CYS MET LEU ALA SER MET ILE PHE ARG LYS SEQRES 19 A 340 GLU PRO PHE PHE HIS GLY HIS ASP ASN TYR ASP GLN LEU SEQRES 20 A 340 VAL ARG ILE ALA LYS VAL LEU GLY THR GLU ASP LEU TYR SEQRES 21 A 340 ASP TYR ILE ASP LYS TYR ASN ILE GLU LEU ASP PRO ARG SEQRES 22 A 340 PHE ASN ASP ILE LEU GLY ARG HIS SER ARG LYS ARG TRP SEQRES 23 A 340 GLU ARG PHE VAL HIS SER GLU ASN GLN HIS LEU VAL SER SEQRES 24 A 340 PRO GLU ALA LEU ASP PHE LEU ASP LYS LEU LEU ARG TYR SEQRES 25 A 340 ASP HIS GLN SER ARG LEU THR ALA ARG GLU ALA MET GLU SEQRES 26 A 340 HIS PRO TYR PHE TYR THR VAL VAL LYS ASP GLN ALA ARG SEQRES 27 A 340 MET GLY HET E3U A 401 44 HETNAM E3U (6AR)-3,4,6A,10-TETRAKIS(OXIDANYL)-6,7-DIHYDROINDENO[2, HETNAM 2 E3U 1-C]CHROMEN-9-ONE FORMUL 2 E3U C16 H12 O6 FORMUL 3 HOH *85(H2 O) HELIX 1 AA1 ASP A 25 HIS A 29 5 5 HELIX 2 AA2 ASN A 35 ASP A 37 5 3 HELIX 3 AA3 LYS A 74 ARG A 89 1 16 HELIX 4 AA4 THR A 129 SER A 149 1 21 HELIX 5 AA5 LYS A 158 HIS A 160 5 3 HELIX 6 AA6 SER A 194 LYS A 198 5 5 HELIX 7 AA7 GLY A 199 VAL A 204 1 6 HELIX 8 AA8 TYR A 211 ARG A 228 1 18 HELIX 9 AA9 ASP A 237 GLY A 250 1 14 HELIX 10 AB1 GLY A 250 ASN A 262 1 13 HELIX 11 AB2 ARG A 268 GLY A 274 1 7 HELIX 12 AB3 ARG A 280 VAL A 285 5 6 HELIX 13 AB4 ASN A 289 VAL A 293 5 5 HELIX 14 AB5 SER A 294 LEU A 305 1 12 HELIX 15 AB6 ASP A 308 ARG A 312 5 5 HELIX 16 AB7 THR A 314 GLU A 320 1 7 HELIX 17 AB8 HIS A 321 TYR A 323 5 3 HELIX 18 AB9 PHE A 324 ASP A 330 1 7 SHEET 1 AA1 5 TYR A 39 ARG A 47 0 SHEET 2 AA1 5 SER A 51 ASN A 58 -1 O VAL A 53 N LEU A 45 SHEET 3 AA1 5 LYS A 64 LEU A 70 -1 O VAL A 65 N ALA A 56 SHEET 4 AA1 5 PRO A 109 GLU A 114 -1 O LEU A 111 N LYS A 68 SHEET 5 AA1 5 LEU A 97 LYS A 102 -1 N VAL A 101 O ALA A 110 SHEET 1 AA2 2 ILE A 152 MET A 153 0 SHEET 2 AA2 2 GLU A 180 PHE A 181 -1 O GLU A 180 N MET A 153 SHEET 1 AA3 2 VAL A 162 ASP A 165 0 SHEET 2 AA3 2 LYS A 170 LEU A 173 -1 O LYS A 170 N ASP A 165 CISPEP 1 GLU A 230 PRO A 231 0 -0.59 SITE 1 AC1 13 VAL A 53 VAL A 66 LYS A 68 ILE A 95 SITE 2 AC1 13 PHE A 113 GLU A 114 TYR A 115 ILE A 116 SITE 3 AC1 13 HIS A 160 MET A 163 ILE A 174 ASP A 175 SITE 4 AC1 13 HOH A 501 CRYST1 51.588 78.823 79.964 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 0.019384 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012687 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012506 0.00000