HEADER LIPID BINDING PROTEIN 09-SEP-10 3OST TITLE STRUCTURE OF THE KINASE ASSOCIATED-1 (KA1) FROM KCC4P COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE KCC4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE ASSOCIATED-1 (KA1) DOMAIN, RESIDUES 917-1036; COMPND 5 EC: 2.7.11.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BREWER'S YEAST,LAGER BEER YEAST,YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: KCC4, YCL024W, YCL24W; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KINASE ASSOCIATED-1(KA1) DOMAIN, TRANSFERASE, LIPID BINDING PROTEIN, KEYWDS 2 MEMBRANE ASSOCIATION, KINASE EXPDTA X-RAY DIFFRACTION AUTHOR K.MORAVCEVIC,M.A.LEMMON REVDAT 4 21-FEB-24 3OST 1 REMARK REVDAT 3 17-JUL-19 3OST 1 REMARK REVDAT 2 05-JAN-11 3OST 1 JRNL REVDAT 1 22-DEC-10 3OST 0 JRNL AUTH K.MORAVCEVIC,J.M.MENDROLA,K.R.SCHMITZ,Y.H.WANG,D.SLOCHOWER, JRNL AUTH 2 P.A.JANMEY,M.A.LEMMON JRNL TITL KINASE ASSOCIATED-1 DOMAINS DRIVE MARK/PAR1 KINASES TO JRNL TITL 2 MEMBRANE TARGETS BY BINDING ACIDIC PHOSPHOLIPIDS. JRNL REF CELL(CAMBRIDGE,MASS.) V. 143 966 2010 JRNL REFN ISSN 0092-8674 JRNL PMID 21145462 JRNL DOI 10.1016/J.CELL.2010.11.028 REMARK 2 REMARK 2 RESOLUTION. 1.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6_289 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) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 14348 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 720 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 26.3358 - 2.8964 0.98 2740 141 0.1656 0.1731 REMARK 3 2 2.8964 - 2.2994 1.00 2745 148 0.1459 0.1924 REMARK 3 3 2.2994 - 2.0088 1.00 2722 154 0.1188 0.1870 REMARK 3 4 2.0088 - 1.8252 1.00 2734 140 0.1200 0.1986 REMARK 3 5 1.8252 - 1.6944 0.98 2687 137 0.1341 0.2153 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 : 0.37 REMARK 3 B_SOL : 66.31 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.380 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) : 3.36290 REMARK 3 B22 (A**2) : -3.91670 REMARK 3 B33 (A**2) : -1.37010 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.41600 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 : 0.008 1011 REMARK 3 ANGLE : 1.144 1377 REMARK 3 CHIRALITY : 0.072 167 REMARK 3 PLANARITY : 0.005 167 REMARK 3 DIHEDRAL : 15.515 391 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 THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3OST COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1000061528. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14366 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04000 REMARK 200 FOR THE DATA SET : 51.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.24600 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX C/D/E REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, PH 7.4, 0.2 M (NH4)2SO4 REMARK 280 PLUS 20% (W/V) PEG3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 29.77950 REMARK 290 SMTRY3 2 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 MET A 910 REMARK 465 HIS A 911 REMARK 465 HIS A 912 REMARK 465 HIS A 913 REMARK 465 HIS A 914 REMARK 465 HIS A 915 REMARK 465 HIS A 916 REMARK 465 LYS A 917 REMARK 465 LYS A 1037 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 918 CD CE NZ REMARK 470 LYS A 927 CE NZ REMARK 470 LYS A 930 CB CG CD CE NZ REMARK 470 GLU A 935 CD OE1 OE2 REMARK 470 LYS A 945 CG CD CE NZ REMARK 470 LYS A 953 CE NZ REMARK 470 LYS A 964 CE NZ REMARK 470 LYS A 978 CE NZ REMARK 470 ASP A 982 CG OD1 OD2 REMARK 470 ARG A 988 NE CZ NH1 NH2 REMARK 470 LYS A1016 CG CD CE NZ REMARK 470 LYS A1020 CG CD 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 ASN A 999 39.83 -145.44 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 SO4 A 1042 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1041 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1038 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1039 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1040 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3OSM RELATED DB: PDB REMARK 900 RELATED ID: 3OSE RELATED DB: PDB DBREF 3OST A 917 1037 UNP P25389 KCC4_YEAST 917 1037 SEQADV 3OST MET A 910 UNP P25389 EXPRESSION TAG SEQADV 3OST HIS A 911 UNP P25389 EXPRESSION TAG SEQADV 3OST HIS A 912 UNP P25389 EXPRESSION TAG SEQADV 3OST HIS A 913 UNP P25389 EXPRESSION TAG SEQADV 3OST HIS A 914 UNP P25389 EXPRESSION TAG SEQADV 3OST HIS A 915 UNP P25389 EXPRESSION TAG SEQADV 3OST HIS A 916 UNP P25389 EXPRESSION TAG SEQRES 1 A 128 MET HIS HIS HIS HIS HIS HIS LYS LYS PRO PRO ASN SER SEQRES 2 A 128 VAL LEU LEU LYS LYS PHE SER LYS GLY LYS ILE LEU GLU SEQRES 3 A 128 LEU GLU ILE HIS ALA LYS ILE PRO GLU LYS ARG LEU TYR SEQRES 4 A 128 GLU GLY LEU HIS LYS LEU LEU GLU GLY TRP LYS GLN TYR SEQRES 5 A 128 GLY LEU LYS ASN LEU VAL PHE ASN ILE THR ASN MET ILE SEQRES 6 A 128 ILE THR GLY LYS LEU VAL ASN ASP SER ILE LEU PHE LEU SEQRES 7 A 128 ARG SER THR LEU PHE GLU ILE MET VAL LEU PRO ASN GLY SEQRES 8 A 128 ASP GLY ARG SER LEU ILE LYS PHE ASN LYS LYS THR GLY SEQRES 9 A 128 SER THR LYS THR LEU THR LYS LEU ALA THR GLU ILE GLN SEQRES 10 A 128 ILE ILE LEU GLN LYS GLU GLY VAL LEU ASP LYS HET SO4 A1042 5 HET SO4 A1041 5 HET GOL A1038 6 HET GOL A1039 6 HET GOL A1040 6 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 GOL 3(C3 H8 O3) FORMUL 7 HOH *106(H2 O) HELIX 1 1 PRO A 920 LEU A 925 1 6 HELIX 2 2 LYS A 926 PHE A 928 5 3 HELIX 3 3 PRO A 943 GLY A 957 1 15 HELIX 4 4 TRP A 958 TYR A 961 5 4 HELIX 5 5 SER A 1014 GLU A 1032 1 19 SHEET 1 A 3 LYS A 932 ILE A 933 0 SHEET 2 A 3 SER A1004 LYS A1010 -1 O LYS A1010 N LYS A 932 SHEET 3 A 3 ILE A 938 ALA A 940 -1 N ALA A 940 O SER A1004 SHEET 1 B 5 LYS A 932 ILE A 933 0 SHEET 2 B 5 SER A1004 LYS A1010 -1 O LYS A1010 N LYS A 932 SHEET 3 B 5 THR A 990 PRO A 998 -1 N GLU A 993 O ASN A1009 SHEET 4 B 5 ILE A 974 LEU A 979 -1 N LEU A 979 O THR A 990 SHEET 5 B 5 LEU A 963 ASN A 969 -1 N VAL A 967 O THR A 976 SITE 1 AC1 4 HOH A 36 HOH A 71 LYS A 964 ASN A 965 SITE 1 AC2 4 LYS A 932 LYS A1010 THR A1015 GOL A1039 SITE 1 AC3 6 HOH A 15 ASN A 921 LEU A 925 GLU A 937 SITE 2 AC3 6 LYS A1007 GOL A1040 SITE 1 AC4 7 LYS A 941 LYS A1010 GLY A1013 SER A1014 SITE 2 AC4 7 THR A1015 LYS A1016 SO4 A1041 SITE 1 AC5 4 HOH A 65 LEU A 934 LYS A1007 GOL A1038 CRYST1 29.373 59.559 37.566 90.00 91.84 90.00 P 1 21 1 2 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 0.034045 0.000000 0.001094 0.00000 SCALE2 0.000000 0.016790 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026634 0.00000