HEADER TRANSCRIPTION 06-JUL-15 5CE7 TITLE STRUCTURE OF A NON-CANONICAL CID OF CTK3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CTD KINASE SUBUNIT GAMMA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CTDK-I GAMMA SUBUNIT,CTD KINASE SUBUNIT 3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 3 ORGANISM_COMMON: FISSION YEAST; SOURCE 4 ORGANISM_TAXID: 4896; SOURCE 5 GENE: CTK3, SPCC4B3.08; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LSG1, CTD KINASE SUBUNIT GAMMA, RIGHT-HANDED SUPERHELIX, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR W.MUEHLBACHER,A.MAYER,M.SUN,M.REMMERT,A.C.CHEUNG,J.NIESSER,J.SOEDING, AUTHOR 2 P.CRAMER REVDAT 4 13-NOV-24 5CE7 1 REMARK REVDAT 3 16-SEP-15 5CE7 1 JRNL REVDAT 2 19-AUG-15 5CE7 1 JRNL REVDAT 1 05-AUG-15 5CE7 0 JRNL AUTH W.MUHLBACHER,A.MAYER,M.SUN,M.REMMERT,A.C.CHEUNG,J.NIESSER, JRNL AUTH 2 J.SOEDING,P.CRAMER JRNL TITL STRUCTURE OF CTK3, A SUBUNIT OF THE RNA POLYMERASE II CTD JRNL TITL 2 KINASE COMPLEX, REVEALS A NONCANONICAL CTD-INTERACTING JRNL TITL 3 DOMAIN FOLD. JRNL REF PROTEINS V. 83 1849 2015 JRNL REFN ESSN 1097-0134 JRNL PMID 26219431 JRNL DOI 10.1002/PROT.24869 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.580 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 20524 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 983 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 47.1329 - 3.8256 1.00 2809 121 0.2001 0.2286 REMARK 3 2 3.8256 - 3.0367 1.00 2790 129 0.2012 0.2642 REMARK 3 3 3.0367 - 2.6528 1.00 2812 140 0.1774 0.2438 REMARK 3 4 2.6528 - 2.4103 1.00 2777 164 0.1712 0.2102 REMARK 3 5 2.4103 - 2.2376 1.00 2754 145 0.1737 0.2405 REMARK 3 6 2.2376 - 2.1056 1.00 2842 130 0.1851 0.2489 REMARK 3 7 2.1056 - 2.0002 1.00 2757 154 0.1916 0.2627 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.390 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 : 0.008 1145 REMARK 3 ANGLE : 1.047 1544 REMARK 3 CHIRALITY : 0.072 168 REMARK 3 PLANARITY : 0.005 197 REMARK 3 DIHEDRAL : 17.952 439 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 5CE7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211399. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97964, 0.98012 ,0.97197 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20524 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 47.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.8900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.930 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, CITRIC ACID, LITHIUM REMARK 280 CHLORIDE, PH 4.0, VAPOR DIFFUSION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 59.52500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.65500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.65500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 89.28750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.65500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.65500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.76250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.65500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.65500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 89.28750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.65500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.65500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.76250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.52500 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 TOTAL BURIED SURFACE AREA: 650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 9.0 KCAL/MOL 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 NZ LYS A 26 O HOH A 301 2.07 REMARK 500 O HOH A 366 O HOH A 367 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 365 O HOH A 366 4565 2.08 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 EPE A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 202 DBREF 5CE7 A 1 140 UNP Q9USJ8 CTK3_SCHPO 1 140 SEQRES 1 A 140 MSE ASP PRO PHE GLU GLY ARG MSE THR PHE LEU GLN LEU SEQRES 2 A 140 LEU GLY LYS LEU ASN ALA SER GLN PHE SER GLN ILE LYS SEQRES 3 A 140 PRO ALA GLN PHE ALA ILE LYS HIS LEU ASP LEU GLU GLU SEQRES 4 A 140 ASP LEU TYR SER CYS ILE TRP GLU GLU LEU GLU SER GLY SEQRES 5 A 140 SER PHE ASN THR ARG VAL ASN ILE MSE TYR PHE VAL ASP SEQRES 6 A 140 THR LEU CYS GLU MSE CYS LEU LYS ASN GLY LEU THR GLY SEQRES 7 A 140 GLY TYR LEU ASN MSE ILE SER ARG ASP ILE CYS LYS LEU SEQRES 8 A 140 VAL GLN ASN VAL ALA PRO ILE GLY ALA ALA GLY ALA ALA SEQRES 9 A 140 ASN ALA PRO GLU VAL ARG LYS VAL LEU GLN SER LEU HIS SEQRES 10 A 140 GLU LYS LYS VAL ILE ASP ASP ASN GLN TYR LYS ASP ALA SEQRES 11 A 140 MSE ALA THR VAL GLU ALA HIS GLU GLN ALA MODRES 5CE7 MSE A 1 MET MODIFIED RESIDUE MODRES 5CE7 MSE A 8 MET MODIFIED RESIDUE MODRES 5CE7 MSE A 61 MET MODIFIED RESIDUE MODRES 5CE7 MSE A 70 MET MODIFIED RESIDUE MODRES 5CE7 MSE A 83 MET MODIFIED RESIDUE MODRES 5CE7 MSE A 131 MET MODIFIED RESIDUE HET MSE A 1 8 HET MSE A 8 8 HET MSE A 61 8 HET MSE A 70 8 HET MSE A 83 8 HET MSE A 131 8 HET EPE A 201 15 HET EPE A 202 15 HETNAM MSE SELENOMETHIONINE HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 2 EPE 2(C8 H18 N2 O4 S) FORMUL 4 HOH *67(H2 O) HELIX 1 AA1 ASP A 2 GLY A 15 1 14 HELIX 2 AA2 SER A 20 SER A 23 5 4 HELIX 3 AA3 GLN A 24 HIS A 34 1 11 HELIX 4 AA4 LEU A 37 GLY A 52 1 16 HELIX 5 AA5 SER A 53 ASN A 74 1 22 HELIX 6 AA6 GLY A 79 ASP A 87 1 9 HELIX 7 AA7 ASP A 87 ALA A 96 1 10 HELIX 8 AA8 GLY A 99 LYS A 119 1 21 HELIX 9 AA9 ASP A 123 ALA A 140 1 18 LINK C MSE A 1 N ASP A 2 1555 1555 1.33 LINK C ARG A 7 N MSE A 8 1555 1555 1.33 LINK C MSE A 8 N THR A 9 1555 1555 1.33 LINK C ILE A 60 N MSE A 61 1555 1555 1.33 LINK C MSE A 61 N TYR A 62 1555 1555 1.33 LINK C GLU A 69 N MSE A 70 1555 1555 1.32 LINK C MSE A 70 N CYS A 71 1555 1555 1.33 LINK C ASN A 82 N MSE A 83 1555 1555 1.33 LINK C MSE A 83 N ILE A 84 1555 1555 1.32 LINK C ALA A 130 N MSE A 131 1555 1555 1.33 LINK C MSE A 131 N ALA A 132 1555 1555 1.33 SITE 1 AC1 5 GLN A 12 LYS A 16 LEU A 35 ASP A 36 SITE 2 AC1 5 GLU A 38 SITE 1 AC2 9 ALA A 19 GLN A 21 GLU A 39 SER A 43 SITE 2 AC2 9 TYR A 62 PRO A 107 GLU A 108 LYS A 111 SITE 3 AC2 9 HOH A 344 CRYST1 51.310 51.310 119.050 90.00 90.00 90.00 P 43 21 2 8 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 0.019489 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019489 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008400 0.00000 HETATM 1 N MSE A 1 35.684 17.757 35.634 1.00 36.28 N ANISOU 1 N MSE A 1 4433 4900 4453 -239 168 -143 N HETATM 2 CA MSE A 1 36.575 18.846 36.005 1.00 29.34 C ANISOU 2 CA MSE A 1 3575 3978 3594 -210 150 -118 C HETATM 3 C MSE A 1 38.036 18.434 35.855 1.00 25.72 C ANISOU 3 C MSE A 1 3129 3476 3167 -226 157 -128 C HETATM 4 O MSE A 1 38.456 17.418 36.409 1.00 29.92 O ANISOU 4 O MSE A 1 3669 3978 3721 -239 168 -148 O HETATM 5 CB MSE A 1 36.312 19.287 37.445 1.00 30.05 C ANISOU 5 CB MSE A 1 3684 4036 3696 -179 138 -107 C HETATM 6 CG MSE A 1 37.160 20.468 37.868 1.00 27.87 C ANISOU 6 CG MSE A 1 3431 3719 3440 -151 121 -84 C HETATM 7 SE MSE A 1 36.880 20.936 39.741 1.00 39.58 SE ANISOU 7 SE MSE A 1 4938 5163 4939 -118 108 -76 SE HETATM 8 CE MSE A 1 35.253 21.979 39.540 1.00 47.35 C ANISOU 8 CE MSE A 1 5905 6198 5889 -90 99 -57 C