HEADER TRANSFERASE/RNA 16-MAY-13 4KR7 TITLE CRYSTAL STRUCTURE OF A 4-THIOURIDINE SYNTHETASE - RNA COMPLEX WITH TITLE 2 BOUND ATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE TRNA SULFURTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SULFUR CARRIER PROTEIN THIS SULFURTRANSFERASE, THIAMINE COMPND 5 BIOSYNTHESIS PROTEIN THII, TRNA 4-THIOURIDINE SYNTHASE; COMPND 6 EC: 2.8.1.4; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: RNA (39-MER); COMPND 11 CHAIN: M, X; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 243274; SOURCE 4 STRAIN: ATCC 43589; SOURCE 5 GENE: AAD36761, THII, TM_1694; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS TRNA MODIFICATION, THIOURIDINE, SULFURTRANSFERASE, ADENYLATION, THUMP KEYWDS 2 DOMAIN, PP-LOOP MOTIF, 4-THIOURIDINE SYNTHESIS, TRANSFERASE-RNA KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.NEUMANN,R.FICNER,K.LAKOMEK REVDAT 4 28-FEB-24 4KR7 1 REMARK SEQADV REVDAT 3 04-SEP-19 4KR7 1 REMARK REVDAT 2 16-JUL-14 4KR7 1 JRNL REVDAT 1 23-APR-14 4KR7 0 JRNL AUTH P.NEUMANN,K.LAKOMEK,P.T.NAUMANN,W.M.ERWIN,C.T.LAUHON, JRNL AUTH 2 R.FICNER JRNL TITL CRYSTAL STRUCTURE OF A 4-THIOURIDINE SYNTHETASE-RNA COMPLEX JRNL TITL 2 REVEALS SPECIFICITY OF TRNA U8 MODIFICATION. JRNL REF NUCLEIC ACIDS RES. V. 42 6673 2014 JRNL REFN ISSN 0305-1048 JRNL PMID 24705700 JRNL DOI 10.1093/NAR/GKU249 REMARK 2 REMARK 2 RESOLUTION. 3.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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) : 3.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 21154 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1058 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 29.3927 - 6.8173 0.95 2581 136 0.1825 0.2015 REMARK 3 2 6.8173 - 5.4222 0.99 2567 135 0.2323 0.3016 REMARK 3 3 5.4222 - 4.7400 1.00 2550 134 0.2115 0.2659 REMARK 3 4 4.7400 - 4.3081 1.00 2555 135 0.2026 0.2604 REMARK 3 5 4.3081 - 4.0001 1.00 2543 133 0.2447 0.2986 REMARK 3 6 4.0001 - 3.7648 1.00 2525 133 0.2683 0.3367 REMARK 3 7 3.7648 - 3.5766 1.00 2511 132 0.3093 0.3702 REMARK 3 8 3.5766 - 3.4211 0.90 2264 120 0.3858 0.4123 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.600 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 76.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 103.0 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 : 0.010 8243 REMARK 3 ANGLE : 0.968 11510 REMARK 3 CHIRALITY : 0.062 1350 REMARK 3 PLANARITY : 0.004 1164 REMARK 3 DIHEDRAL : 18.736 3386 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 77:162 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.4714 43.5177 7.4757 REMARK 3 T TENSOR REMARK 3 T11: 0.5873 T22: 0.7037 REMARK 3 T33: 0.7217 T12: 0.0133 REMARK 3 T13: -0.0265 T23: -0.0303 REMARK 3 L TENSOR REMARK 3 L11: 4.9021 L22: 4.6657 REMARK 3 L33: 3.6315 L12: 0.0357 REMARK 3 L13: 1.2797 L23: 0.9878 REMARK 3 S TENSOR REMARK 3 S11: -0.3683 S12: 0.2748 S13: 0.7367 REMARK 3 S21: 0.2875 S22: 0.2888 S23: 0.5244 REMARK 3 S31: 0.1692 S32: 0.2400 S33: -0.0142 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 3:76 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.5845 21.4078 8.9659 REMARK 3 T TENSOR REMARK 3 T11: 0.6038 T22: 0.8090 REMARK 3 T33: 0.5532 T12: 0.0678 REMARK 3 T13: 0.0261 T23: 0.0228 REMARK 3 L TENSOR REMARK 3 L11: 2.2226 L22: 3.1300 REMARK 3 L33: 2.5365 L12: 1.1503 REMARK 3 L13: 0.5248 L23: 0.4312 REMARK 3 S TENSOR REMARK 3 S11: 0.1443 S12: -0.4283 S13: -0.0019 REMARK 3 S21: 0.4365 S22: -0.2105 S23: 0.2182 REMARK 3 S31: 0.3808 S32: 0.0091 S33: 0.2264 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND ( RESID 163:388 OR RESID 401:402 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.3591 -4.0758 -13.0931 REMARK 3 T TENSOR REMARK 3 T11: 0.6142 T22: 0.5002 REMARK 3 T33: 0.7202 T12: 0.1067 REMARK 3 T13: 0.1565 T23: -0.0364 REMARK 3 L TENSOR REMARK 3 L11: 2.2377 L22: 1.9178 REMARK 3 L33: 1.7256 L12: -0.2469 REMARK 3 L13: -0.3170 L23: 0.7180 REMARK 3 S TENSOR REMARK 3 S11: -0.3180 S12: -0.0681 S13: -0.6696 REMARK 3 S21: -0.0458 S22: 0.2062 S23: -0.1204 REMARK 3 S31: 0.4575 S32: 0.2692 S33: 0.1850 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN B AND RESID 77:162 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.2871 34.0806 -43.9568 REMARK 3 T TENSOR REMARK 3 T11: 1.1188 T22: 0.9314 REMARK 3 T33: 1.0566 T12: -0.2799 REMARK 3 T13: 0.3975 T23: -0.0238 REMARK 3 L TENSOR REMARK 3 L11: 2.3852 L22: 2.5571 REMARK 3 L33: 2.0577 L12: 0.3946 REMARK 3 L13: 0.2019 L23: -0.0624 REMARK 3 S TENSOR REMARK 3 S11: -0.0170 S12: 0.3145 S13: 0.6991 REMARK 3 S21: -0.8362 S22: 0.3896 S23: -0.5281 REMARK 3 S31: -0.4293 S32: -0.6460 S33: -0.1834 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN B AND RESID 3:76 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.5231 17.7906 -41.8930 REMARK 3 T TENSOR REMARK 3 T11: 0.9019 T22: 0.8902 REMARK 3 T33: 0.6254 T12: -0.1346 REMARK 3 T13: 0.0819 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 2.6199 L22: 2.6879 REMARK 3 L33: 2.6478 L12: -0.4742 REMARK 3 L13: -0.0339 L23: -0.8187 REMARK 3 S TENSOR REMARK 3 S11: -0.3487 S12: 0.6154 S13: -0.0656 REMARK 3 S21: -0.6977 S22: 0.3209 S23: 0.0463 REMARK 3 S31: 0.4283 S32: -0.3022 S33: 0.0947 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN B AND ( RESID 163:388 OR RESID 401:402 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): -42.1475 5.6828 -16.7423 REMARK 3 T TENSOR REMARK 3 T11: 0.4994 T22: 0.5233 REMARK 3 T33: 0.7036 T12: -0.0137 REMARK 3 T13: 0.1088 T23: -0.1146 REMARK 3 L TENSOR REMARK 3 L11: 2.8305 L22: 2.3792 REMARK 3 L33: 3.1514 L12: 0.2179 REMARK 3 L13: -0.7782 L23: -0.4635 REMARK 3 S TENSOR REMARK 3 S11: -0.2891 S12: 0.0143 S13: -0.1441 REMARK 3 S21: 0.0225 S22: 0.1195 S23: 0.4076 REMARK 3 S31: 0.0551 S32: -0.3726 S33: 0.1857 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN M AND RESID 1:39 ) REMARK 3 ORIGIN FOR THE GROUP (A): -42.3671 27.6458 7.4265 REMARK 3 T TENSOR REMARK 3 T11: 1.0780 T22: 1.0341 REMARK 3 T33: 1.0572 T12: -0.1424 REMARK 3 T13: 0.0356 T23: 0.1204 REMARK 3 L TENSOR REMARK 3 L11: 3.6852 L22: 2.2613 REMARK 3 L33: 1.1569 L12: 0.3928 REMARK 3 L13: 0.7005 L23: -0.1836 REMARK 3 S TENSOR REMARK 3 S11: -0.3791 S12: -0.3562 S13: 0.5581 REMARK 3 S21: -0.2849 S22: 0.4197 S23: 0.8661 REMARK 3 S31: 0.2805 S32: -0.0618 S33: -0.0426 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN X AND RESID 1:39 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.5291 7.5867 -39.2507 REMARK 3 T TENSOR REMARK 3 T11: 1.5949 T22: 1.3155 REMARK 3 T33: 1.2365 T12: -0.2233 REMARK 3 T13: 0.0768 T23: -0.1781 REMARK 3 L TENSOR REMARK 3 L11: 0.5427 L22: 5.8860 REMARK 3 L33: 0.1251 L12: -0.1804 REMARK 3 L13: 0.0982 L23: 0.8721 REMARK 3 S TENSOR REMARK 3 S11: 0.3712 S12: 0.3642 S13: -0.0585 REMARK 3 S21: 1.1270 S22: -0.0397 S23: -1.8844 REMARK 3 S31: 0.2418 S32: -0.3010 S33: -0.3465 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT WAS BASED ON SIMULATED REMARK 3 ANNEALING IN TORSION ANGLE SPACE AND GROUPED B-FACTORS. REMARK 4 REMARK 4 4KR7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079692. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.814000 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21271 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.420 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.67000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 MICRO-LITER OF THII-RNA COMPLEX REMARK 280 SOLUTION AT 10 MG/ML IN A BUFFER CONSISTING OF 150 MM AMMONIUM REMARK 280 SULFATE, 20MM TRIS/HCL PH 7.5 WAS MIXED WITH 3 MICRO-LITER OF REMARK 280 FRESHLY PREPARED RESERVOIR SOLUTION (2.0 M SODIUM FORMATE, 100 REMARK 280 MM SODIUM CITRATE, 2 MM DTT), VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 292K, PH 4.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 51.58500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.59000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.61000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.59000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 51.58500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 56.61000 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 300 REMARK: BIOLOGICAL UNIT IS A HOMODIMER. THERE IS 1 BIOLOGICAL REMARK 300 UNIT IN THE ASYMMETRIC UNIT (CHAINS A & B) 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, M, X 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 1 REMARK 465 GLU A 2 REMARK 465 MET B 1 REMARK 465 GLU B 2 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 LEU B 180 O2' ATP B 401 2.08 REMARK 500 O ILE A 32 OG1 THR A 36 2.16 REMARK 500 O ILE B 32 OG1 THR B 36 2.18 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 NZ LYS A 350 O2' C X 38 3544 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU B 181 CA - CB - CG ANGL. DEV. = 14.4 DEGREES REMARK 500 A M 23 C1' - O4' - C4' ANGL. DEV. = -4.8 DEGREES REMARK 500 A M 23 O4' - C1' - N9 ANGL. DEV. = 12.9 DEGREES REMARK 500 G X 10 O3' - P - OP2 ANGL. DEV. = 6.8 DEGREES REMARK 500 U X 13 N1 - C2 - O2 ANGL. DEV. = 5.0 DEGREES REMARK 500 U X 13 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 U X 13 C2 - N1 - C1' ANGL. DEV. = 8.7 DEGREES REMARK 500 C X 14 C6 - N1 - C2 ANGL. DEV. = -2.6 DEGREES REMARK 500 C X 14 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 C X 14 C6 - N1 - C1' ANGL. DEV. = -9.3 DEGREES REMARK 500 C X 14 C2 - N1 - C1' ANGL. DEV. = 12.0 DEGREES REMARK 500 C X 15 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 C X 15 C2 - N1 - C1' ANGL. DEV. = 7.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 TYR A 11 53.34 -143.59 REMARK 500 SER A 12 106.55 -17.34 REMARK 500 PHE A 24 -72.12 -53.15 REMARK 500 ASN A 54 10.21 59.48 REMARK 500 ASP A 79 102.19 -55.72 REMARK 500 GLN A 106 77.02 -119.83 REMARK 500 PRO A 210 38.34 -92.75 REMARK 500 SER A 213 -173.88 -66.98 REMARK 500 GLU A 214 -86.72 -63.85 REMARK 500 PRO A 255 -174.49 -58.51 REMARK 500 SER A 343 -177.72 58.64 REMARK 500 PHE A 346 -88.21 -59.27 REMARK 500 HIS A 357 130.97 -179.96 REMARK 500 LEU B 16 13.01 57.79 REMARK 500 LYS B 17 -77.41 -52.32 REMARK 500 ASN B 20 94.63 -60.17 REMARK 500 PHE B 24 -71.87 -54.38 REMARK 500 ASP B 79 104.98 -59.97 REMARK 500 ARG B 197 20.05 -78.31 REMARK 500 PRO B 255 -177.10 -59.48 REMARK 500 GLN B 291 -33.12 -138.45 REMARK 500 GLN B 295 43.15 -152.28 REMARK 500 ILE B 337 44.20 38.55 REMARK 500 LYS B 338 159.69 69.65 REMARK 500 PHE B 346 -17.32 86.00 REMARK 500 SER B 356 -158.64 -154.06 REMARK 500 HIS B 357 132.06 178.73 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 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A 401 O3B REMARK 620 2 ATP A 401 O3G 52.8 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4KR6 RELATED DB: PDB REMARK 900 RELATED ID: 4KR9 RELATED DB: PDB DBREF 4KR7 A 1 388 UNP Q9X220 THII_THEMA 1 388 DBREF 4KR7 B 1 388 UNP Q9X220 THII_THEMA 1 388 DBREF 4KR7 M 1 39 PDB 4KR7 4KR7 1 39 DBREF 4KR7 X 1 39 PDB 4KR7 4KR7 1 39 SEQADV 4KR7 GLU A 2 UNP Q9X220 LYS 2 ENGINEERED MUTATION SEQADV 4KR7 GLU B 2 UNP Q9X220 LYS 2 ENGINEERED MUTATION SEQRES 1 A 388 MET GLU GLU LEU ARG VAL TYR ILE VAL ARG TYR SER GLU SEQRES 2 A 388 ILE GLY LEU LYS GLY LYS ASN ARG LYS ASP PHE GLU GLU SEQRES 3 A 388 ALA LEU ARG ARG ASN ILE GLU ARG VAL THR GLY MET LYS SEQRES 4 A 388 VAL LYS ARG GLN TRP GLY ARG PHE LEU ILE PRO ILE ASP SEQRES 5 A 388 GLU ASN VAL THR LEU ASP ASP LYS LEU LYS LYS ILE PHE SEQRES 6 A 388 GLY ILE GLN ASN PHE SER LYS GLY PHE LEU VAL SER HIS SEQRES 7 A 388 ASP PHE GLU GLU VAL LYS LYS TYR SER LEU ILE ALA VAL SEQRES 8 A 388 LYS GLU LYS LEU GLU LYS GLY ASN TYR ARG THR PHE LYS SEQRES 9 A 388 VAL GLN ALA LYS LYS ALA TYR LYS GLU TYR LYS LYS GLY SEQRES 10 A 388 VAL TYR GLU ILE ASN SER GLU LEU GLY ALA LEU ILE LEU SEQRES 11 A 388 LYS ASN PHE LYS GLU LEU SER VAL ASP VAL ARG ASN PRO SEQRES 12 A 388 ASP PHE VAL LEU GLY VAL GLU VAL ARG PRO GLU GLY VAL SEQRES 13 A 388 LEU ILE PHE THR ASP ARG VAL GLU CYS TYR GLY GLY LEU SEQRES 14 A 388 PRO VAL GLY THR GLY GLY LYS ALA VAL LEU LEU LEU SER SEQRES 15 A 388 GLY GLY ILE ASP SER PRO VAL ALA GLY TRP TYR ALA LEU SEQRES 16 A 388 LYS ARG GLY VAL LEU ILE GLU SER VAL THR PHE VAL SER SEQRES 17 A 388 PRO PRO PHE THR SER GLU GLY ALA VAL GLU LYS VAL ARG SEQRES 18 A 388 ASP ILE LEU ARG VAL LEU ARG GLU PHE SER GLY GLY HIS SEQRES 19 A 388 PRO LEU ARG LEU HIS ILE VAL ASN LEU THR LYS LEU GLN SEQRES 20 A 388 LEU GLU VAL LYS LYS ARG VAL PRO ASP LYS TYR SER LEU SEQRES 21 A 388 ILE MET TYR ARG ARG SER MET PHE ARG ILE ALA GLU LYS SEQRES 22 A 388 ILE ALA GLU GLU THR GLY ALA VAL ALA PHE TYR THR GLY SEQRES 23 A 388 GLU ASN ILE GLY GLN VAL ALA SER GLN THR LEU GLU ASN SEQRES 24 A 388 LEU TRP SER ILE GLU SER VAL THR THR ARG PRO VAL ILE SEQRES 25 A 388 ARG PRO LEU SER GLY PHE ASP LYS THR GLU ILE VAL GLU SEQRES 26 A 388 LYS ALA LYS GLU ILE GLY THR TYR GLU ILE SER ILE LYS SEQRES 27 A 388 PRO TYR GLN ASP SER CYS VAL PHE PHE ALA PRO LYS ASN SEQRES 28 A 388 PRO ALA THR ARG SER HIS PRO SER ILE LEU GLU LYS LEU SEQRES 29 A 388 GLU GLN GLN VAL PRO ASP LEU PRO VAL LEU GLU GLU GLU SEQRES 30 A 388 ALA PHE THR SER ARG LYS VAL GLU VAL ILE GLU SEQRES 1 B 388 MET GLU GLU LEU ARG VAL TYR ILE VAL ARG TYR SER GLU SEQRES 2 B 388 ILE GLY LEU LYS GLY LYS ASN ARG LYS ASP PHE GLU GLU SEQRES 3 B 388 ALA LEU ARG ARG ASN ILE GLU ARG VAL THR GLY MET LYS SEQRES 4 B 388 VAL LYS ARG GLN TRP GLY ARG PHE LEU ILE PRO ILE ASP SEQRES 5 B 388 GLU ASN VAL THR LEU ASP ASP LYS LEU LYS LYS ILE PHE SEQRES 6 B 388 GLY ILE GLN ASN PHE SER LYS GLY PHE LEU VAL SER HIS SEQRES 7 B 388 ASP PHE GLU GLU VAL LYS LYS TYR SER LEU ILE ALA VAL SEQRES 8 B 388 LYS GLU LYS LEU GLU LYS GLY ASN TYR ARG THR PHE LYS SEQRES 9 B 388 VAL GLN ALA LYS LYS ALA TYR LYS GLU TYR LYS LYS GLY SEQRES 10 B 388 VAL TYR GLU ILE ASN SER GLU LEU GLY ALA LEU ILE LEU SEQRES 11 B 388 LYS ASN PHE LYS GLU LEU SER VAL ASP VAL ARG ASN PRO SEQRES 12 B 388 ASP PHE VAL LEU GLY VAL GLU VAL ARG PRO GLU GLY VAL SEQRES 13 B 388 LEU ILE PHE THR ASP ARG VAL GLU CYS TYR GLY GLY LEU SEQRES 14 B 388 PRO VAL GLY THR GLY GLY LYS ALA VAL LEU LEU LEU SER SEQRES 15 B 388 GLY GLY ILE ASP SER PRO VAL ALA GLY TRP TYR ALA LEU SEQRES 16 B 388 LYS ARG GLY VAL LEU ILE GLU SER VAL THR PHE VAL SER SEQRES 17 B 388 PRO PRO PHE THR SER GLU GLY ALA VAL GLU LYS VAL ARG SEQRES 18 B 388 ASP ILE LEU ARG VAL LEU ARG GLU PHE SER GLY GLY HIS SEQRES 19 B 388 PRO LEU ARG LEU HIS ILE VAL ASN LEU THR LYS LEU GLN SEQRES 20 B 388 LEU GLU VAL LYS LYS ARG VAL PRO ASP LYS TYR SER LEU SEQRES 21 B 388 ILE MET TYR ARG ARG SER MET PHE ARG ILE ALA GLU LYS SEQRES 22 B 388 ILE ALA GLU GLU THR GLY ALA VAL ALA PHE TYR THR GLY SEQRES 23 B 388 GLU ASN ILE GLY GLN VAL ALA SER GLN THR LEU GLU ASN SEQRES 24 B 388 LEU TRP SER ILE GLU SER VAL THR THR ARG PRO VAL ILE SEQRES 25 B 388 ARG PRO LEU SER GLY PHE ASP LYS THR GLU ILE VAL GLU SEQRES 26 B 388 LYS ALA LYS GLU ILE GLY THR TYR GLU ILE SER ILE LYS SEQRES 27 B 388 PRO TYR GLN ASP SER CYS VAL PHE PHE ALA PRO LYS ASN SEQRES 28 B 388 PRO ALA THR ARG SER HIS PRO SER ILE LEU GLU LYS LEU SEQRES 29 B 388 GLU GLN GLN VAL PRO ASP LEU PRO VAL LEU GLU GLU GLU SEQRES 30 B 388 ALA PHE THR SER ARG LYS VAL GLU VAL ILE GLU SEQRES 1 M 39 G C C C G G A U A G U G U SEQRES 2 M 39 C C U U G G G A A A C C A SEQRES 3 M 39 A G U C C G G G C A C C A SEQRES 1 X 39 G C C C G G A U A G U G U SEQRES 2 X 39 C C U U G G G A A A C C A SEQRES 3 X 39 A G U C C G G G C A C C A HET ATP A 401 31 HET MG A 402 1 HET ATP B 401 31 HET MG B 402 1 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 5 ATP 2(C10 H16 N5 O13 P3) FORMUL 6 MG 2(MG 2+) HELIX 1 1 GLY A 18 GLY A 37 1 20 HELIX 2 2 LEU A 57 LYS A 63 1 7 HELIX 3 3 ASP A 79 GLY A 98 1 20 HELIX 4 4 GLY A 117 PHE A 133 1 17 HELIX 5 5 ILE A 185 ARG A 197 1 13 HELIX 6 6 GLY A 215 SER A 231 1 17 HELIX 7 7 LEU A 243 VAL A 254 1 12 HELIX 8 8 TYR A 258 GLY A 279 1 22 HELIX 9 9 THR A 296 SER A 305 1 10 HELIX 10 10 ASP A 319 ILE A 330 1 12 HELIX 11 11 THR A 332 LYS A 338 1 7 HELIX 12 12 SER A 359 GLU A 365 1 7 HELIX 13 13 GLN A 366 VAL A 368 5 3 HELIX 14 14 ASP A 370 SER A 381 1 12 HELIX 15 15 ASN B 20 GLY B 37 1 18 HELIX 16 16 LEU B 57 LYS B 63 1 7 HELIX 17 17 ASP B 79 GLY B 98 1 20 HELIX 18 18 GLY B 117 PHE B 133 1 17 HELIX 19 19 ILE B 185 ARG B 197 1 13 HELIX 20 20 SER B 213 SER B 231 1 19 HELIX 21 21 LEU B 243 VAL B 254 1 12 HELIX 22 22 TYR B 258 GLY B 279 1 22 HELIX 23 23 VAL B 292 GLN B 295 5 4 HELIX 24 24 THR B 296 SER B 305 1 10 HELIX 25 25 ASP B 319 ILE B 330 1 12 HELIX 26 26 THR B 332 ILE B 337 1 6 HELIX 27 27 HIS B 357 GLU B 365 1 9 HELIX 28 28 GLN B 366 VAL B 368 5 3 HELIX 29 29 ASP B 370 SER B 381 1 12 SHEET 1 A 7 LYS A 41 GLN A 43 0 SHEET 2 A 7 ARG A 46 PRO A 50 -1 O ARG A 46 N GLN A 43 SHEET 3 A 7 LEU A 4 ARG A 10 -1 N VAL A 9 O PHE A 47 SHEET 4 A 7 ASN A 69 VAL A 76 -1 O SER A 71 N ILE A 8 SHEET 5 A 7 GLY A 155 PHE A 159 -1 O VAL A 156 N VAL A 76 SHEET 6 A 7 PHE A 145 ARG A 152 -1 N GLU A 150 O LEU A 157 SHEET 7 A 7 PHE A 103 LYS A 109 1 N LYS A 108 O VAL A 149 SHEET 1 B 5 LYS A 41 GLN A 43 0 SHEET 2 B 5 ARG A 46 PRO A 50 -1 O ARG A 46 N GLN A 43 SHEET 3 B 5 LEU A 4 ARG A 10 -1 N VAL A 9 O PHE A 47 SHEET 4 B 5 ASN A 69 VAL A 76 -1 O SER A 71 N ILE A 8 SHEET 5 B 5 VAL A 163 GLU A 164 -1 O VAL A 163 N PHE A 70 SHEET 1 C 6 VAL A 311 ILE A 312 0 SHEET 2 C 6 ALA A 282 TYR A 284 1 N PHE A 283 O ILE A 312 SHEET 3 C 6 LYS A 176 LEU A 180 1 N VAL A 178 O ALA A 282 SHEET 4 C 6 LEU A 200 VAL A 207 1 O GLU A 202 N ALA A 177 SHEET 5 C 6 LEU A 236 ASN A 242 1 O HIS A 239 N THR A 205 SHEET 6 C 6 LYS A 383 ILE A 387 -1 O GLU A 385 N LEU A 238 SHEET 1 D 8 LYS B 41 GLN B 43 0 SHEET 2 D 8 ARG B 46 PRO B 50 -1 O ARG B 46 N GLN B 43 SHEET 3 D 8 LEU B 4 ARG B 10 -1 N VAL B 9 O PHE B 47 SHEET 4 D 8 ASN B 69 VAL B 76 -1 O ASN B 69 N ARG B 10 SHEET 5 D 8 GLY B 155 PHE B 159 -1 O ILE B 158 N PHE B 74 SHEET 6 D 8 PHE B 145 ARG B 152 -1 N GLU B 150 O LEU B 157 SHEET 7 D 8 THR B 102 LYS B 109 1 N LYS B 108 O VAL B 149 SHEET 8 D 8 SER B 137 VAL B 138 1 O SER B 137 N PHE B 103 SHEET 1 E 5 LYS B 41 GLN B 43 0 SHEET 2 E 5 ARG B 46 PRO B 50 -1 O ARG B 46 N GLN B 43 SHEET 3 E 5 LEU B 4 ARG B 10 -1 N VAL B 9 O PHE B 47 SHEET 4 E 5 ASN B 69 VAL B 76 -1 O ASN B 69 N ARG B 10 SHEET 5 E 5 VAL B 163 GLU B 164 -1 O VAL B 163 N PHE B 70 SHEET 1 F 6 VAL B 311 ILE B 312 0 SHEET 2 F 6 ALA B 282 TYR B 284 1 N PHE B 283 O ILE B 312 SHEET 3 F 6 LYS B 176 LEU B 180 1 N VAL B 178 O ALA B 282 SHEET 4 F 6 LEU B 200 VAL B 207 1 O VAL B 204 N LEU B 179 SHEET 5 F 6 LEU B 236 ASN B 242 1 O HIS B 239 N THR B 205 SHEET 6 F 6 LYS B 383 ILE B 387 -1 O GLU B 385 N LEU B 238 LINK O3B ATP A 401 MG MG A 402 1555 1555 2.74 LINK O3G ATP A 401 MG MG A 402 1555 1555 2.74 LINK O1G ATP B 401 MG MG B 402 1555 1555 2.94 CISPEP 1 PRO A 209 PRO A 210 0 3.91 CISPEP 2 PRO B 209 PRO B 210 0 0.46 SITE 1 AC1 18 LEU A 180 LEU A 181 SER A 182 GLY A 184 SITE 2 AC1 18 ILE A 185 ASP A 186 SER A 187 VAL A 204 SITE 3 AC1 18 THR A 205 PHE A 206 ARG A 264 MET A 267 SITE 4 AC1 18 THR A 285 GLY A 286 GLU A 287 GLN A 291 SITE 5 AC1 18 GLN A 295 MG A 402 SITE 1 AC2 1 ATP A 401 SITE 1 AC3 14 LEU B 180 LEU B 181 SER B 182 ASP B 186 SITE 2 AC3 14 SER B 187 VAL B 204 PHE B 206 ARG B 264 SITE 3 AC3 14 MET B 267 GLY B 286 GLU B 287 ASN B 288 SITE 4 AC3 14 LYS B 320 MG B 402 SITE 1 AC4 1 ATP B 401 CRYST1 103.170 113.220 133.180 90.00 90.00 90.00 P 21 21 21 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 0.009693 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008832 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007509 0.00000