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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
