HEADER TRANSFERASE 19-SEP-16 5LX2 TITLE LT 14-3-3 IN COMPLEX WITH PI4KIIIB PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: KLTH0G14146P; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PHOSPHATIDYLINOSITOL 4-KINASE BETA; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: UNP RESIDUES 304-309; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACHANCEA THERMOTOLERANS (STRAIN ATCC 56472 / SOURCE 3 CBS 6340 / NRRL Y-8284); SOURCE 4 ORGANISM_COMMON: YEAST; SOURCE 5 ORGANISM_TAXID: 559295; SOURCE 6 GENE: KLTH0G14146G; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS PHOSPHOSERIN, KINASE, REGULATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR E.BOURA,A.EISENREICHOVA REVDAT 3 17-JAN-24 5LX2 1 REMARK REVDAT 2 26-JUL-17 5LX2 1 REVDAT 1 16-NOV-16 5LX2 0 SPRSDE 16-NOV-16 5LX2 5LI5 JRNL AUTH E.BOURA,A.EISENREICHOVA JRNL TITL LT 14-3-3 IN COMPLEX WITH PI4KIIIB PEPTIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 10040 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 503 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 44.4975 - 4.0927 0.98 2517 133 0.1766 0.2356 REMARK 3 2 4.0927 - 3.2488 0.99 2371 125 0.1852 0.2292 REMARK 3 3 3.2488 - 2.8382 0.98 2358 124 0.2531 0.3217 REMARK 3 4 2.8382 - 2.5788 0.98 2291 121 0.2734 0.3667 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.040 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 1927 REMARK 3 ANGLE : 0.524 2608 REMARK 3 CHIRALITY : 0.023 299 REMARK 3 PLANARITY : 0.002 333 REMARK 3 DIHEDRAL : 11.443 716 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 5LX2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1200001501. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-AUG-15 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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10043 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.579 REMARK 200 RESOLUTION RANGE LOW (A) : 44.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.16710 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 1.04500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.560 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: 5LHO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES, PEG 8000, ETHYLENE GLYCOL, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 32.03150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 61.83550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.03150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 61.83550 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 64.06300 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 123.67100 REMARK 350 BIOMT3 2 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 MET A 1 REMARK 465 SER A 2 REMARK 465 GLN A 3 REMARK 465 GLU A 239 REMARK 465 ALA A 240 REMARK 465 GLY A 241 REMARK 465 GLN A 242 REMARK 465 ASP A 243 REMARK 465 GLU A 244 REMARK 465 GLN A 245 REMARK 465 GLN A 246 REMARK 465 PRO A 247 REMARK 465 ALA A 248 REMARK 465 GLU A 249 REMARK 465 GLY A 250 REMARK 465 ALA A 251 REMARK 465 GLN A 252 REMARK 465 GLU A 253 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 70 CG CD CE NZ REMARK 470 LYS A 74 CG CD CE NZ REMARK 470 ASP A 75 CG OD1 OD2 REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 GLU A 78 CG CD OE1 OE2 REMARK 470 LYS B 297 CE NZ 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 LYS A 74 -12.55 62.38 REMARK 500 GLU A 78 -113.56 57.08 REMARK 500 HIS A 109 -64.57 -106.36 REMARK 500 ILE A 186 -62.66 -95.81 REMARK 500 PRO B 296 57.96 -91.74 REMARK 500 REMARK 500 REMARK: NULL DBREF 5LX2 A 1 253 UNP C5DN49 C5DN49_LACTC 1 253 DBREF1 5LX2 B 292 297 UNP A0A0B4J1S8_HUMAN DBREF2 5LX2 B A0A0B4J1S8 304 309 SEQRES 1 A 253 MET SER GLN SER ARG GLU ASP SER VAL TYR LEU ALA LYS SEQRES 2 A 253 LEU ALA GLU GLN ALA GLU ARG TYR GLU GLU MET VAL ASP SEQRES 3 A 253 SER MET LYS ALA VAL ALA SER SER GLY GLN GLU LEU SER SEQRES 4 A 253 VAL GLU GLU ARG ASN LEU LEU SER VAL ALA TYR LYS ASN SEQRES 5 A 253 VAL ILE GLY ALA ARG ARG ALA SER TRP ARG ILE VAL SER SEQRES 6 A 253 SER ILE GLU GLN LYS GLU GLU ALA LYS ASP LYS SER GLU SEQRES 7 A 253 HIS GLN VAL LYS LEU ILE ARG ASP TYR ARG SER LYS ILE SEQRES 8 A 253 GLU THR GLU LEU THR LYS ILE CYS ASP ASP ILE LEU SER SEQRES 9 A 253 VAL LEU ASP THR HIS LEU ILE PRO SER ALA THR THR GLY SEQRES 10 A 253 GLU SER LYS VAL PHE TYR TYR LYS MET LYS GLY ASP TYR SEQRES 11 A 253 HIS ARG TYR LEU ALA GLU PHE SER SER GLY GLU VAL ARG SEQRES 12 A 253 ASP LYS ALA THR ASN ALA SER LEU GLU ALA TYR LYS THR SEQRES 13 A 253 ALA SER GLU ILE ALA THR THR GLU LEU PRO PRO THR HIS SEQRES 14 A 253 PRO ILE ARG LEU GLY LEU ALA LEU ASN PHE SER VAL PHE SEQRES 15 A 253 TYR TYR GLU ILE GLN ASN SER PRO ASP LYS ALA CYS HIS SEQRES 16 A 253 LEU ALA LYS GLN ALA PHE ASP ASP ALA ILE ALA GLU LEU SEQRES 17 A 253 ASP THR LEU SER GLU GLU SER TYR LYS ASP SER THR LEU SEQRES 18 A 253 ILE MET GLN LEU LEU ARG ASP ASN LEU THR LEU TRP THR SEQRES 19 A 253 SER ASP MET SER GLU ALA GLY GLN ASP GLU GLN GLN PRO SEQRES 20 A 253 ALA GLU GLY ALA GLN GLU SEQRES 1 B 6 THR ALA SEP ASN PRO LYS MODRES 5LX2 SEP B 294 SER MODIFIED RESIDUE HET SEP B 294 10 HETNAM SEP PHOSPHOSERINE HETSYN SEP PHOSPHONOSERINE FORMUL 2 SEP C3 H8 N O6 P FORMUL 3 HOH *30(H2 O) HELIX 1 AA1 SER A 4 ALA A 18 1 15 HELIX 2 AA2 ARG A 20 SER A 33 1 14 HELIX 3 AA3 SER A 39 GLU A 72 1 34 HELIX 4 AA4 GLU A 78 HIS A 109 1 32 HELIX 5 AA5 HIS A 109 ALA A 114 1 6 HELIX 6 AA6 THR A 116 SER A 138 1 23 HELIX 7 AA7 GLY A 140 LEU A 165 1 26 HELIX 8 AA8 HIS A 169 ILE A 186 1 18 HELIX 9 AA9 SER A 189 LEU A 208 1 20 HELIX 10 AB1 ASP A 209 LEU A 211 5 3 HELIX 11 AB2 SER A 212 MET A 237 1 26 LINK C ALA B 293 N SEP B 294 1555 1555 1.33 LINK C SEP B 294 N ASN B 295 1555 1555 1.33 CRYST1 64.063 123.671 38.688 90.00 90.00 90.00 P 21 21 2 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 0.015610 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008086 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025848 0.00000