HEADER LIPID BINDING PROTEIN 06-NOV-20 7KO6 TITLE C1B DOMAIN OF PROTEIN KINASE C IN COMPLEX WITH INGENOL-3-ANGELATE AND TITLE 2 PHOSPHOCHOLINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN KINASE C DELTA TYPE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C1B DOMAIN; COMPND 5 SYNONYM: NPKC-DELTA; COMPND 6 EC: 2.7.11.13; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: PRKCD, RCG_42255; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS C1, LIPID-BINDING, DIACYLGLYCEROL-BINDING, ZN2+ FINGER, LIPID BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.S.KATTI,I.V.KRIEGER REVDAT 3 18-OCT-23 7KO6 1 REMARK REVDAT 2 13-JUL-22 7KO6 1 JRNL REVDAT 1 04-MAY-22 7KO6 0 JRNL AUTH S.S.KATTI,I.V.KRIEGER,J.ANN,J.LEE,J.C.SACCHETTINI, JRNL AUTH 2 T.I.IGUMENOVA JRNL TITL STRUCTURAL ANATOMY OF PROTEIN KINASE C C1 DOMAIN JRNL TITL 2 INTERACTIONS WITH DIACYLGLYCEROL AND OTHER AGONISTS. JRNL REF NAT COMMUN V. 13 2695 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 35577811 JRNL DOI 10.1038/S41467-022-30389-2 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 4815 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.360 REMARK 3 FREE R VALUE TEST SET COUNT : 258 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 28.5600 - 2.2700 1.00 2310 146 0.1662 0.1916 REMARK 3 2 2.2600 - 1.8000 1.00 2247 112 0.1963 0.2906 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.54 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 : 0.011 500 REMARK 3 ANGLE : 2.187 680 REMARK 3 CHIRALITY : 0.095 69 REMARK 3 PLANARITY : 0.008 81 REMARK 3 DIHEDRAL : 41.937 96 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 7KO6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1000252795. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-20 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : BRUKER PHOTON II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SAINT REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4819 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 57.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.54 REMARK 200 R MERGE (I) : 0.11440 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.7600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.790 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1PTQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SCREEN CONDITION: 0.2 M AMMONIUM REMARK 280 ACETATE, 0.1 M SODIUM PHOSPHATE, 30% ISOPROPANOL, PH 6.8, DROP REMARK 280 CONDITION: PROTEIN: 2 MM IN MES PH 6.5, 150 MM KCL, REMARK 280 PHOSPHATIDYLCHOLINE: 20 MM, INGENOL-3-ANGELATE: 2.5 MM, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 17.19200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 12.95450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 17.19200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 12.95450 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 405 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 417 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 452 LIES ON A SPECIAL POSITION. 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 281 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 278 41.59 -102.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 231 ND1 REMARK 620 2 CYS A 261 SG 108.1 REMARK 620 3 CYS A 264 SG 106.3 108.1 REMARK 620 4 CYS A 280 SG 113.8 108.1 112.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 244 SG REMARK 620 2 CYS A 247 SG 110.8 REMARK 620 3 HIS A 269 ND1 102.7 96.8 REMARK 620 4 CYS A 272 SG 115.7 112.8 116.2 REMARK 620 N 1 2 3 DBREF1 7KO6 A 229 281 UNP A0A140UHX0_RAT DBREF2 7KO6 A A0A140UHX0 229 281 SEQRES 1 A 53 MET PRO HIS ARG PHE LYS VAL TYR ASN TYR MET SER PRO SEQRES 2 A 53 THR PHE CYS ASP HIS CYS GLY SER LEU LEU TRP GLY LEU SEQRES 3 A 53 VAL LYS GLN GLY LEU LYS CYS GLU ASP CYS GLY MET ASN SEQRES 4 A 53 VAL HIS HIS LYS CYS ARG GLU LYS VAL ALA ASN LEU CYS SEQRES 5 A 53 GLY HET ZN A 301 1 HET ZN A 302 1 HET WUD A 303 31 HET XP5 A 304 32 HETNAM ZN ZINC ION HETNAM WUD INGENOL-3-ANGELATE HETNAM XP5 (4S,7R)-7-(HEPTANOYLOXY)-4-HYDROXY-N,N,N-TRIMETHYL-10- HETNAM 2 XP5 OXO-3,5,9-TRIOXA-4-PHOSPHAHEXADECAN-1-AMINIUM 4-OXIDE HETSYN WUD INGENOL MEBUTATE; (1AR,2S,5R,5AS,6S,8AS,9R,10AR)-5,5A- HETSYN 2 WUD DIHYDROXY-4-(HYDROXYMETHYL)-1,1,7,9-TETRAMETHYL-11- HETSYN 3 WUD OXO-1A,2,5,5A,6,9,10,10A-OCTAHYDRO-1H-2,8A- HETSYN 4 WUD METHANOCYCLOPENTA[A]CYCLOPROPA[E][10]ANNULEN-6-YL HETSYN 5 WUD (2Z)-2-METHYLBUT-2-ENOATE FORMUL 2 ZN 2(ZN 2+) FORMUL 4 WUD C25 H34 O6 FORMUL 5 XP5 C22 H45 N O8 P 1+ FORMUL 6 HOH *53(H2 O) SHEET 1 AA1 3 PHE A 233 TYR A 236 0 SHEET 2 AA1 3 GLY A 258 CYS A 261 -1 O GLY A 258 N TYR A 236 SHEET 3 AA1 3 ASN A 267 VAL A 268 -1 O VAL A 268 N LEU A 259 LINK ND1 HIS A 231 ZN ZN A 301 1555 1555 2.09 LINK SG CYS A 244 ZN ZN A 302 1555 1555 2.34 LINK SG CYS A 247 ZN ZN A 302 1555 1555 2.31 LINK SG CYS A 261 ZN ZN A 301 1555 1555 2.33 LINK SG CYS A 264 ZN ZN A 301 1555 1555 2.32 LINK ND1 HIS A 269 ZN ZN A 302 1555 1555 2.14 LINK SG CYS A 272 ZN ZN A 302 1555 1555 2.31 LINK SG CYS A 280 ZN ZN A 301 1555 1555 2.29 CRYST1 34.384 25.909 57.731 90.00 98.39 90.00 C 1 2 1 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 0.029083 0.000000 0.004291 0.00000 SCALE2 0.000000 0.038597 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017509 0.00000