PDB Short entry for 4FKD HEADER TRANSFERASE 13-JUN-12 4FKD TITLE IDENTIFICATION OF THE ACTIVATOR BINDING RESIDUES IN THE SECOND TITLE 2 CYSTEINE-RICH REGULATORY DOMAIN OF PROTEIN KINASE C THETA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN KINASE C THETA TYPE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NPKC-THETA; COMPND 5 EC: 2.7.11.13; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PRKCQ, PKCQ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PKC THETA, SECOND CYSTEINE RICH REGULATORY DOMAIN, ACTIVATOR BINDING KEYWDS 2 SITE, ZINC FINGER, KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.M.RAHMAN,S.SHANKER,N.E.LEWIN,B.V.V.PRASAD,P.M.BLUMBERG,J.DAS REVDAT 3 28-FEB-24 4FKD 1 REMARK SEQADV LINK REVDAT 2 19-JUN-13 4FKD 1 JRNL REVDAT 1 23-JAN-13 4FKD 0 JRNL AUTH G.M.RAHMAN,S.SHANKER,N.E.LEWIN,N.KEDEI,C.S.HILL,B.V.PRASAD, JRNL AUTH 2 P.M.BLUMBERG,J.DAS JRNL TITL IDENTIFICATION OF THE ACTIVATOR BINDING RESIDUES IN THE JRNL TITL 2 SECOND CYSTEINE-RICH REGULATORY DOMAIN OF PROTEIN KINASE C JRNL TITL 3 THETA. JRNL REF BIOCHEM.J. V. 451 33 2013 JRNL REFN ISSN 0264-6021 JRNL PMID 23289588 JRNL DOI 10.1042/BJ20121307 REMARK 2 REMARK 2 RESOLUTION. 1.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.4 REMARK 3 NUMBER OF REFLECTIONS : 7550 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.400 REMARK 3 FREE R VALUE TEST SET COUNT : 332 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 28.5182 - 2.0576 0.88 3632 162 0.1580 0.1849 REMARK 3 2 2.0576 - 1.6333 0.89 3586 170 0.2067 0.2490 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.61 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 41.89 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.700 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) : -3.19440 REMARK 3 B22 (A**2) : -3.19440 REMARK 3 B33 (A**2) : 6.38870 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 : 0.010 532 REMARK 3 ANGLE : 1.030 705 REMARK 3 CHIRALITY : 0.068 74 REMARK 3 PLANARITY : 0.004 90 REMARK 3 DIHEDRAL : 11.493 187 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 1:7) REMARK 3 ORIGIN FOR THE GROUP (A): 14.3470 -6.9100 3.9808 REMARK 3 T TENSOR REMARK 3 T11: 0.1266 T22: 0.1230 REMARK 3 T33: 0.1127 T12: -0.0228 REMARK 3 T13: -0.0150 T23: -0.0214 REMARK 3 L TENSOR REMARK 3 L11: 0.8359 L22: 0.1626 REMARK 3 L33: 0.0434 L12: 0.1154 REMARK 3 L13: -0.0767 L23: -0.0487 REMARK 3 S TENSOR REMARK 3 S11: 0.1507 S12: -0.1969 S13: 0.1032 REMARK 3 S21: 0.0498 S22: -0.0075 S23: 0.0352 REMARK 3 S31: -0.0377 S32: -0.0670 S33: -0.0367 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 8:20) REMARK 3 ORIGIN FOR THE GROUP (A): 10.2937 -26.7518 -0.0817 REMARK 3 T TENSOR REMARK 3 T11: 0.0893 T22: 0.0898 REMARK 3 T33: 0.1205 T12: -0.0087 REMARK 3 T13: -0.0057 T23: 0.0193 REMARK 3 L TENSOR REMARK 3 L11: 0.1711 L22: 0.1617 REMARK 3 L33: 0.1016 L12: 0.0228 REMARK 3 L13: 0.0207 L23: 0.0674 REMARK 3 S TENSOR REMARK 3 S11: -0.0633 S12: -0.1628 S13: 0.0136 REMARK 3 S21: 0.0118 S22: 0.0383 S23: -0.1359 REMARK 3 S31: -0.0801 S32: -0.0215 S33: 0.0130 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 21:48) REMARK 3 ORIGIN FOR THE GROUP (A): 5.0879 -27.7143 -3.1975 REMARK 3 T TENSOR REMARK 3 T11: 0.0719 T22: 0.0721 REMARK 3 T33: 0.0825 T12: -0.0070 REMARK 3 T13: -0.0053 T23: -0.0074 REMARK 3 L TENSOR REMARK 3 L11: 0.2160 L22: 0.3198 REMARK 3 L33: 0.1339 L12: 0.0840 REMARK 3 L13: 0.0461 L23: -0.0316 REMARK 3 S TENSOR REMARK 3 S11: -0.0595 S12: -0.0032 S13: -0.0760 REMARK 3 S21: -0.0036 S22: 0.0319 S23: -0.0813 REMARK 3 S31: -0.0092 S32: -0.0096 S33: -0.0052 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 49:65) REMARK 3 ORIGIN FOR THE GROUP (A): 11.2409 -17.5717 -3.9603 REMARK 3 T TENSOR REMARK 3 T11: 0.1185 T22: 0.1123 REMARK 3 T33: 0.1049 T12: -0.0157 REMARK 3 T13: -0.0221 T23: -0.0058 REMARK 3 L TENSOR REMARK 3 L11: 0.1634 L22: 0.2251 REMARK 3 L33: 0.3131 L12: 0.1714 REMARK 3 L13: 0.0729 L23: 0.1927 REMARK 3 S TENSOR REMARK 3 S11: -0.1027 S12: 0.0317 S13: 0.0924 REMARK 3 S21: -0.0795 S22: 0.0182 S23: 0.1323 REMARK 3 S31: -0.0815 S32: 0.0925 S33: 0.0250 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 4FKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000073007. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 7.2 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 FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7559 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 28.514 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.4 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.11500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 MR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M LITHIUM ACETATE AND 20% PEG REMARK 280 3350, PH 7.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 9.04000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.08000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 13.56000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 22.60000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 4.52000 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 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 O HOH A 294 O HOH A 312 2.17 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 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 10 ND1 REMARK 620 2 CYS A 40 SG 111.3 REMARK 620 3 CYS A 43 SG 104.4 108.3 REMARK 620 4 CYS A 59 SG 108.0 110.2 114.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 23 SG REMARK 620 2 CYS A 26 SG 111.4 REMARK 620 3 HIS A 48 ND1 101.0 98.1 REMARK 620 4 CYS A 51 SG 113.4 115.1 116.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 102 DBREF 4FKD A 10 59 UNP Q02111 KPCT_MOUSE 232 281 SEQADV 4FKD GLY A 1 UNP Q02111 EXPRESSION TAG SEQADV 4FKD SER A 2 UNP Q02111 EXPRESSION TAG SEQADV 4FKD ARG A 3 UNP Q02111 EXPRESSION TAG SEQADV 4FKD ARG A 4 UNP Q02111 EXPRESSION TAG SEQADV 4FKD ALA A 5 UNP Q02111 EXPRESSION TAG SEQADV 4FKD SER A 6 UNP Q02111 EXPRESSION TAG SEQADV 4FKD VAL A 7 UNP Q02111 EXPRESSION TAG SEQADV 4FKD GLY A 8 UNP Q02111 EXPRESSION TAG SEQADV 4FKD SER A 9 UNP Q02111 EXPRESSION TAG SEQADV 4FKD GLU A 60 UNP Q02111 EXPRESSION TAG SEQADV 4FKD PHE A 61 UNP Q02111 EXPRESSION TAG SEQADV 4FKD ILE A 62 UNP Q02111 EXPRESSION TAG SEQADV 4FKD VAL A 63 UNP Q02111 EXPRESSION TAG SEQADV 4FKD THR A 64 UNP Q02111 EXPRESSION TAG SEQADV 4FKD ASP A 65 UNP Q02111 EXPRESSION TAG SEQRES 1 A 65 GLY SER ARG ARG ALA SER VAL GLY SER HIS ARG PHE LYS SEQRES 2 A 65 VAL TYR ASN TYR LYS SER PRO THR PHE CYS GLU HIS CYS SEQRES 3 A 65 GLY THR LEU LEU TRP GLY LEU ALA ARG GLN GLY LEU LYS SEQRES 4 A 65 CYS ASP ALA CYS GLY MET ASN VAL HIS HIS ARG CYS GLN SEQRES 5 A 65 THR LYS VAL ALA ASN LEU CYS GLU PHE ILE VAL THR ASP HET ZN A 101 1 HET ZN A 102 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) FORMUL 4 HOH *130(H2 O) HELIX 1 1 HIS A 48 VAL A 55 5 8 SHEET 1 A 2 SER A 2 VAL A 7 0 SHEET 2 A 2 CYS A 59 THR A 64 -1 O CYS A 59 N VAL A 7 SHEET 1 B 3 PHE A 12 TYR A 15 0 SHEET 2 B 3 GLY A 37 CYS A 40 -1 O LYS A 39 N LYS A 13 SHEET 3 B 3 ASN A 46 VAL A 47 -1 O VAL A 47 N LEU A 38 LINK ND1 HIS A 10 ZN ZN A 102 1555 1555 2.17 LINK SG CYS A 23 ZN ZN A 101 1555 1555 2.40 LINK SG CYS A 26 ZN ZN A 101 1555 1555 2.37 LINK SG CYS A 40 ZN ZN A 102 1555 1555 2.35 LINK SG CYS A 43 ZN ZN A 102 1555 1555 2.39 LINK ND1 HIS A 48 ZN ZN A 101 1555 1555 2.17 LINK SG CYS A 51 ZN ZN A 101 1555 1555 2.34 LINK SG CYS A 59 ZN ZN A 102 1555 1555 2.32 SITE 1 AC1 4 CYS A 23 CYS A 26 HIS A 48 CYS A 51 SITE 1 AC2 4 HIS A 10 CYS A 40 CYS A 43 CYS A 59 CRYST1 65.850 65.850 27.120 90.00 90.00 120.00 P 61 6 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 0.015186 0.008768 0.000000 0.00000 SCALE2 0.000000 0.017535 0.000000 0.00000 SCALE3 0.000000 0.000000 0.036873 0.00000